Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaacacttaacaccctttctttctttctttagctattaatattttcattcatggctttctatagtggcagtaaaaagagtttggactttccacctcacctaacctttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
Basic information
species | Glycine max |
transcript | GLYMA12G35530.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaaaaacacttaacaccctttctttctttctttagctattaatattttcattcatggctttctatagtggcagtaaaaagagtttgg-actttccacctcaccta-acctttgt--ttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
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-------------------------ctttatatcaacccttcacatgagtgacca-gtccttgttcggttctaaaacagagtcctccttactctgtttgtaactttcacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA
upper sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaaaaacacttaacaccctttctttctttctttagctattaatattttcattcatggctttct-atagtggcagtaaaaagagtttggactttccacctcacctaacctttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
| | | | || | ||| || |||| | || || |||| || || | || || || ||||||||||||||||||||| ||||||||||| ||| | |||||| | ||||| || || || | ||||| || || || ||||| ||||| ||
--------------------------------------gtaagaaaatacaaaactaacttacttgtagttcttttgtaa-----ttaaggtttctgaaatctttactctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA
upper sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
gtaaaaacacttaacaccctttctttctttctttagctattaatattttcattcatggctttctatagtggcagtaaaaagagtttggactttccacctcacctaacctttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
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-----------------gttggtaccacctacctacccttctacattttctctcaaacacccacacaatc-cattaa------tttatag---ccattttttttaacataca-----aacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA
upper sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S159_57V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------gtaaaaacacttaacaccctttctttctttctttagctattaatattttcatt--catggctttctatagtggcagtaaaaagagttt----ggactttccacctcacctaacctttgttt---ttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
|| | | | || | || || | | | || || | | | | | | || | || || | | | | | || || | | |||||| || ||| |||||| | | | || ||||| ||||||||||| || ||| |||| ||| ||||||| ||||| || ||||||||||| || || ||||| || ||
gtatgcattgtttatttaaattaaattcaactttttaggatgctgcaccatggatttcattaggagtacaggatactgcggcaacactagattaattccttgaaaaacctttacagtacttgattcttgtttgttttctcagTGAAAGCAACGTTTGGGGAGAAGGAGTGGTACTTTTTTAGCCTACGAGACCGAAAGTATCCAACGGGATTAAGAACCAACAGAGCCACTGAGAAGGGCTA
upper sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ22540 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------gtaaaaacacttaacaccctttct---ttctttctttagctattaatatttt-cattcatggctttctatag----tggcagtaaaaa--------gagtt---tggactttccacctc-----acctaacctttgttttt-----------ggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
|| | | | ||| || || ||||| | | || | || |||||||||| ||| | | ||| | | | ||||| ||||| |||| | || |||||||| || |||||||||||| || ||||||||||| || ||||||||||| ||||| | ||| | |||||||| || ||| | | || ||| |||| || || || || ||
gtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGGAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA
upper sequence: GLYMA12G35530.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------gtaaaaacacttaacaccctttctttctttct--------ttagctattaatat------tttcattcatggctttctatag----tggcagtaaaaa--------gagtt---tggactttccacctc-----acctaacctttgttttt-----------ggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
| | | || || ||| || ||| || | | ||| | || |||||||||| ||| | | ||| | | | ||||| ||||| |||| | || |||||||| || |||||||||||| || ||||||||||| || ||||||||||| ||||| | ||| | |||||||| || ||| | | || ||| |||| || || || || ||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggcagtaaaaagagtttggactttccacctcacctaacctttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
acctaac putative branch site (score: 2)
cctttgttttt CT-rich tract
tttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaacacttaacaccctttctttctttctttagctattaatattttcattcatggctttctatagtggcagtaaaaagagtttggactttccacctcacctaacctttgtttttggcagAGAAAGCTAAGATGGGAGAGAAAGAGTGGTACTTCTTCAGCTTACGTGACAGAAAGTACCCAACTGGGTTAAGAACCAATAGGGCTACTGAAGCTGGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG