Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
Basic information
species | Glycine max |
transcript | GLYMA07G05220.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
--------------gt-aaaatgcacaaga-ctcgtcctctagcttttttttatcattgtttccatga-aaataaatcatttgactaaaattttctcattt---ttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
|| |||| ||||||| || || | || || | | | ||| || | | | | |||| | | | || ||||||||| || || ||||| ||||||||||| || |||||||| |||||||| ||||||||||| || || |||||||| ||||| ||||| ||||||||||
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC
upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T03 (Zea mays), 3'ss of exon 7
----gtaaaat-gcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
|| || | | ||| || ||| || |||||| || |||| |||| || | | ||||| |||| || |||||||| || |||||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||||||||| |||||||||||||||||||| |
ggctgtgaatccgtaaaaggttcatcc---agtttttttcc-----tgcacacatgttaatatttc--tgaaacaaaatattcta--ttgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC
upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 7
--------------gtaaaat-gcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
|| || | | ||| || ||| || |||||| || |||| |||| || | | ||||| |||| || |||||||| || |||||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||||||||| |||||||||||||||||||| |
gtatatctagggctgtgaatccgtaaaaggttcatcc---agtttttttcc-----tgcacacatgttaatatttc--tgaaacaaaatattcta--ttgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC
upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
gtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaat----catttgactaaaat---tttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
|| | | | || ||| | || | || | ||| |||| | | | ||| | || |||| || || | |||||||| || |||||||| || |||||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| ||||||||||| |
---gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC
upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
---gtaaaatgcacaagactcgtcctctagcttttttt-tatcattgtttccatgaa--aataaatcatttgactaaaattttctcatttt-tagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
|| ||| | | | | ||| ||| | | |||||| | || || | |||| | || | | | ||||||| || || || || || || |||||||||||||||||||| ||||| || || ||||| || ||||||||||| |||||||| ||||||||||| |
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
----------------------gtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
| | ||| ||| | | || | | | | |||| || ||| | || || ||| | ||| | |||||||||||||||||||||| |||||||| ||||||||||| || ||||| ||||||||||| || ||||| ||||| | || ||||| ||||||||||
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattctcatggtgcaacctgtccatgttact----------tgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
upper sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 7
---gtaaaatgcacaagactcgtcctctagcttttttttat---cattgtttccatgaaaataaatcatttgactaaaatttt------ctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
| | |||| | ||| | | | ||| | | | | | | | ||| | | | ||| || | ||||||| ||||||||||| || |||||||||||||||||||| || ||||| ||||||||||| || || || ||||| | || ||||| || |||||||
ccgccagtgtattgtttactcaaacgctaagtactgtgtattcacgtggcctacttcgatgcttatcgtggtgcgatttgtttatggaacttgtgagcagATGGCCCGTTCAAAGAAAGCGTGCATTGTGTTTTTTGATGAGGTAGATGCCATTGGAGGTGCTCGTTTCGACGATGGGTTGGGAGGTGATAACGAGGTTCMapped 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|16346898|gb|BI972493.1|BI972493EST: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG ATGGCTCGTTCAAAGAAGGCATGCATTGTGNTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtaaaatgca ... tcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
gactaaa putative branch site (score: 2)
ttttctcattttt CT-rich tract
aaaataaatcatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG