Sequence
atgc intronic sequence ATGC exonic sequence...caatcacaaatagaaatggaaaacacaatgcgacttttattttctagtctaagttgtatttggctgattcttgatgtttctatattgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC
Basic information
species | Glycine max |
transcript | GLYMA05G27840.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G27840.1 (Glycine max), 3'ss of exon 12
lower sequence: 13114.m00153 (Oryza sativa), 3'ss of exon 15
--caatcacaaatagaaatggaaaacacaatgcgacttttattt-tctagtctaagttgtatttggctgattcttgatgtttctatattgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC
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ttttgtgttatacagacccttctattgttatattgtggatattcgtttatgatactgtaaatgggactga--ctaagttataatttactgcct-tgtaaacagTGAAGGAGCAGGTGGTGGTCATGCTCCAGACATTATCAAAGTATGTGGAGTGAAAAATGTGTTACCCTCTTCAACAAATCCAACTCGGCCATTTACTTTG
upper sequence: GLYMA05G27840.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 12
caatcacaaatagaaatggaa-aacacaatgcgacttttattttctagtctaagttgtatttggctgattcttgat-gtttctatattgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC
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-tattgttgtctactttgtagtgtcaatatttatctgtgatatgtgttaatggattgtacctgtcaattttctcatcatgttcttactgtct-tgtggacagTGAAGGTGCTGGTGGCGGTCATGCTCCAGACATCATCAAAGTTTGTGGGGTAAAAAATGTGTTGCCCTCTTCAACAAATCCTACCCGGCCATTTACTTCG
upper sequence: GLYMA05G27840.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 12
------caa--tcacaaatagaaatggaaaacaca-atgcgacttttattttcta-gtctaagttg---tatttggctgattcttgatgtttctatattgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC
|| || || | ||| | | || |||| | || | | || || | | |||| || | || || || || || || |||||||||||| |||||||| ||||| ||||||||||| | ||| ||||| |||| ||||| || || |||||||| ||||||||||| || | ||
gttcatcagcttctcacctcttcatgcacctctcagatgcttccttcactgcttatgtttgaagcaaaatattgaagtgctatttttgtttgttaaatcattc---tggacagTGAAGGTGCTGGTGGTGGACATGCACCAGATATCATTAGAGTTTGTGGAGTGAAAAATGTACTCCCGTCATCAACCAACCCAACACGGCCATATACGAAA
upper sequence: GLYMA05G27840.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 12
-----caatcacaaatagaaatggaaaacacaatgcgacttttattttctagtctaagttgtatttggctgattcttgatgtttctat-attgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC
||| | | | | | | | || | |||||| || | || || | |||| | | | |||||| | | | | | | ||| ||||||||||||| ||||||||||||||||||||||||||||||||||||||| |||| |||||||| |||||||| |||||||||||||| ||||| || |
ttttctaattttctgaaaataagatagattctata-gccttttacattttggt-----ttctttttgtcacacttttgatgcatatgtcggtatctttttgtgcagTGAAGGTGCTGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTGTGAAAAATGTTCTACCCTCATCCACAAACCCAACACGGCCTTTCACTTCCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|298164365|gb|HO014010.1|HO014010EST: GAACATAGCATTGCAGCATTTAAAGGAAGAACTATTCATACTTACCACAG TGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTAT
genomic: GAACATAGCATTGCAGCATTTAAAGGAAGAACTATTCATACTTACCACAGgtataatgct ... acttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtctaagttgtatttggctgattcttgatgtttctatattgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC
tcttgat putative branch site (score: 4)
tttactt putative PPT
tttctatattgttta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatcacaaatagaaatggaaaacacaatgcgacttttattttctagtctaagttgtatttggctgattcttgatgtttctatattgtttacttgagcagTGAAGGTGCAGGTGGTGGTCATGCTCCAGATATCATCAAAGTATGTGGTATGAAGAATGTTCTGCCCTCATCAACAAACCCAACACGCCCTTTAACACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
caatcac
- - - - aatagaaa
- - - - - - - - -ggaaaac
- - - - - - - - - - - - acaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga