2005, NucleaRDB.
The pairwise alignment has been generated with the "genewise" program of the Wise2 package. The output shows the protein sequence on the first line, followed by a line indicating the similarity level of the match, followed by 4 lines representing the DNA sequence; The DNA sequence descending in triplets, each triplet being a codon. The translation of each codon is shown above it.
Between the two protein sequences a line indicating the similarity of the match is printed. "+" indicates a conservative mismatch while "- "indicates a dramatic one. Mismatches are indicated by "***" in the left column in addition to "!" at the relevant position(s).
genewise $Name: wise2-2-0 $ (unreleased release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyright
Query protein: ESR2_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence RNAJ2602_2
Strand: forward
Start/End (protein) default
Gene Paras: human.gf
Codon Table: codon.table
Subs error: 1e-05
Indel error: 1e-05
Model splice? model
Model codon bias? flat
Model intron bias? tied
Null model syn
Algorithm 623
genewise output
Score 1295.41 bits over entire alignment
Scores as bits over a synchronous coding model
Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info.
Warning: protein length=530 (x3=1590) and cDNA length=1650
ESR2_RAT 1 MEIKNSPSSLSSPASYNCSQSILPLEHGPIYIPSSYVDNRHEYSAMTFY
MEIKNSPSSLSSPASYNCSQSILPLEHGPIYIPSSYVDNRHEYSAMTFY
MEIKNSPSSLSSPASYNCSQSILPLEHGPIYIPSSYVDNRHEYSAMTFY
RNAJ2602_2 58 agaaatctacatcgttatactacccgcgcatactttggaccgttgaatt
tataacccgtgccccaaggacttctaagctatcccataagaaacctcta
ggcacaggcttcttctctcgccacggcccccctcccaccctgtatgacc
ESR2_RAT 50 SPAVMNYSVPGSTSNLDGGPVRLSTSPNVLWPTSGHLSPLATHCQSSLL
SPAVMNYSVPGSTSNLDGGPVR STSPNVLWPTSGHLSPLATHCQSSLL
SPAVMNYSVPGSTSNLDGGPVRQSTSPNVLWPTSGHLSPLATHCQSSLL
RNAJ2602_2 205 acggaatagcgaaaacgggcgccaaacagctcatgcctctgactcttcc
gccttaagtcggcgataggctgagcgcattgcccgatcctccagacctt
tttggccttcccctcgctgtcagcacatgagattgcgttagctcaagcc
ESR2_RAT 99 YAEPQKSPWCEARSLEHTLPVNRETLKRKLSGSSCASPVTSPNAKRDAH
YAEPQKSPWCEARSLEHTLPVNRETLKRKLSGSSCASPVTSPNAKRDAH
YAEPQKSPWCEARSLEHTLPVNRETLKRKLSGSSCASPVTSPNAKRDAH
RNAJ2602_2 352 tggccaacttggatcgcatcgaagacaaacagaatgacgaacagaaggc
acacaagcggacgctaactctagactagatgggggcgctcgcacagaca
taatagttgtaaaaagccatacagaggggttgcttccttttacaggttc
ESR2_RAT 148 FCPVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKN
FC VCSDYASGYHYGVW CEGCKAFFKRSIQGHNDYICPATNQCTIDKN
FCAVCSDYASGYHYGVWPCEGCKAFFKRSIQGHNDYICPATNQCTIDKN
RNAJ2602_2 499 ttggtagtgtgtctggtctggtagttaaaacgcagtatcgaactaagaa
tgctggaaccgaaagtgcgaggacttaggtagaaaatgcccaagctaaa
ccccccttatgttcctgataatgcttaactaattttctacgtgtcacgc
ESR2_RAT 197 RRKSCQACRLRKCYEVGMVKCGSRRERCGYRIVRRQRSSSEQVHCLSKA
RRKSCQACRLRKCYEVGMVKCGSRRERCGYRIVRRQRSSSEQVHCLSKA
RRKSCQACRLRKCYEVGMVKCGSRRERCGYRIVRRQRSSSEQVHCLSKA
RNAJ2602_2 646 ccaatcgtcccattgggagatgtaagctgtcagcacaatagcgctcaag
ggaggacggtgagaatgttaggcggagggagttggaggcgaatagtgac
gtaccgccatcgttaaagcgtacgaagtgctaggggattcggaccgcac
ESR2_RAT 246 KRNGGHAPRVKELLLSTLSPEQLVLTLLEAEPPNVLVSRPSMPFTEASM
KRNGGHAPRVKELLLSTLSPEQLVLTLLEAEPPNVLVSRPSMPFTEASM
KRNGGHAPRVKELLLSTLSPEQLVLTLLEAEPPNVLVSRPSMPFTEASM
RNAJ2602_2 793 aaaggcgccgagcccaatacgccgcaccgggccagcgaccaactaggta
agaggaccgtaatttgctgcaatttcttacaccatttggcgtctcacct
gactgcacggggaggccgtagaggcccgataactgggctccgcccgccg
ESR2_RAT 295 MMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGL
MMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGL
MMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGL
RNAJ2602_2 940 aatcaacggagcgcaagtgaaacgtggcactgcgcctgattaggcaggc
ttctcatcaaattattggcaatcgttatgttaatgttagggtattttgt
ggcctgggcgaggcgtcgcgactctggccggcacgcaaccggggaggag
ESR2_RAT 344 MWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKL
MWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKL
MWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKL
RNAJ2602_2 1087 atctagccgacatgcgcgcgagggatgggacgatgaccgaatatcgtac
tggctaacgatttccatttagaagagtagttattatttccccgtgatat
ggcccccccgctctccctgcgtgggcaagtgactcgcggggagctgaac
ESR2_RAT 393 QHKEYLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVI
QHKEYLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVI
QHKEYLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVI
RNAJ2602_2 1234 ccagtctgagaaccataatctgtgacgggaacacacccaggaggcgtga
aaaaatgtacttttacgtactcccaaacagggatcattactcacttgtt
gcggtctggcgccccctgccgttacggaatcgggacagcggatcgcggt
ESR2_RAT 442 AKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMKCKNVVPVYDL
AKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMKCKNVVPVYDL
AKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMKCKNVVPVYDL
RNAJ2602_2 1381 gaagattccctgccgaccacctcgacaaaagagcccaaataaggcgtgc
caggtccaaactgtcatttttcatgatgaagtaattgtagaattctaat
ggttcccgggacagcccggtttccgcctcgcgatgccggcatgcggtcg
ESR2_RAT 491 LLEMLNAHTLRGYKSSISGSECSSTEDSKNKESSQNLQSQ
LLEMLNAHTLRGYK SISGSECSSTEDSKNKESSQNLQSQ
LLEMLNAHTLRGYKPSISGSECSSTEDSKNKESSQNLQSQ
RNAJ2602_2 1528 ccgacagcaccgtactatgtgtataggaaaagatcacctc
ttattacactggaacctcgcaggccaagaaaagcaataca
gggggttcgtagcgcacggtgccaagctgcagccgcagtg
//
cmbi.kun.nl), 18-Feb-2005