Sequence
atgc intronic sequence ATGC exonic sequence...atactttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttgactggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA13G34970.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
--atact--ttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttgactggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
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ctgttctgctagtatcattcggtagt-gtttttagctcaaggacaaacctttgc--ttttggaaggtaatattgctaatggcttttaattttgaattgtg-tagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 4
-atactttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttg--actggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
|| || | ||| | || ||| || | | | | | | | | ||| | | |||| | | | ||| | | | ||||||||||| ||||| || || ||||||||||||||||||||||| ||| |||| || || |||||||||
tttaaattttatggcaaaatattctctttgaaaaatta--cattgattaaagggtgagcatttgtactgctggtctgctgctaatgatttcaaactgtt-cagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAATTCTGAAGGGTACAATGAGAAG
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 8
atactttgtgcaattaaaaaatcacttggagttctaaatta--gtactctacagctctt-catctttgactggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
| |||| || | || | | ||||||| | | | | | | || | | | | | || | | | | | | |||||||||||||||||||||||| ||||||||||| || || |||||||| | || || ||||||||||||
--aacttgt-taagaattttattatgttgagttctcgcctgtgatggtttggtgttattatacaactttcggactgtatttgctaatgatataaagttgacagACATTTGTAGGAACACCATTTTGGATGGCACCAGAAGTGATTCAGAACTCCGAAGGTTATAATGAGAAG
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 8
atactttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttgact--ggatacatattttttttt-ttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
| | | || | ||| | | |||| | | | | || | | || || | || | | | | | | ||| | || |||||| ||||||||||| ||||| ||||||||||| || ||||||||||| | || || ||||||||||||
---atcaatttgaacaacatctcatctttacttctctgctgatggtttgcaattttcactcattcatctgggttgcgtgcgctgatatgttaaagaatgacagACTTTTGTAGGAACCCCATTTTGGATGGCACCAGAAGTTATTCAGAACTCAGAAGGGTATAATGAGAAG
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 8
atactttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttgactggatacatatttttttttttatatc-------ataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
| || || || | | | ||| | | | ||||| | | | |||| |||||||| | || | || ||||||||||||||||||||||||||||||||| || ||||| ||||||||| | || |||||||||||||||
-----gctaggaaccaatgaacatgtctaaaagttgaat--ggatcgaatgcctcttacttcatttcatgatatatatttttacactaatgtgtttaacaatgacagACATTTGTAGGAACACCATTCTGGATGGCTCCAGAGGTAATTCAGAATTCAGAAGGATATAATGAGAAG
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S59_173V6.2 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------atactttgtgcaattaaaaaatcacttggagttctaaattagtactcta-cagct--cttcatctttgactggatacatattttt-----ttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTG---ATGGATATAATGAGAAG
| || | ||| | || || | || | | | || | | | | || ||| || || | || | || | | || || ||||||||||| ||||| |||||||||||||| || ||||| || ||||| ||| |||| || |||||||||
gtcagttgacttctcaactgtatgtggctttttttgaaagagtagccttatccagcatattggaaccgagtctgtatgcggatgaaccatgtgagcggtttgttacgtggtcttaaaattggtgattttgtctaagaatgaaccgatttaattggaagtctgacatgtcgctgcagACATTTGTTGGAACTCCATTCTGGATGGCGCCAGAGGTCATACAGAACTCTGGAGATGGCTACAATGAGAAG
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------atactttgtgcaattaaaa-aatcacttggagttctaaattagtactctacagctcttcatctttga-ctggatacatatttt-------------tttttttatatcataa----------cagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTG---ATGGATATAATGAGAAG
| | |||||| |||| | ||||| || | || | ||| ||| ||| ||||| || ||| || | | | | || || | ||||| ||||| ||||| |||||||||||||| || |||||||| ||||| ||| |||| || ||||||||
gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgta-tctgttattctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ15774 (Selaginella moellendorffii), 3'ss of exon 7
atactttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttgactggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
||| | | | || |||| | | | | | || | | | ||||||||||| || |||||||||||||||||||| ||||| || || ||| | |||||||||||||| |||
-----------------------------------------gtaagttttaaga-tacacctttttataaggaagaagctaactcggta-acgaaatcagACATTTGTCGGGACACCATTCTGGATGGCACCCGAGGTGATCCAAAATTCAGATGGATATAATGAAAAG
upper sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 7
atactttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttgactggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
||| | || | || |||| | | | | | || | | | ||||||||||| || |||||||||||||||||||| ||||| || || ||| | |||||||||||||| |||
-----------------------------------------gtaagtttaagata--cacctttttataaggaagaagctaactcggta-acgaaatcagACATTTGTCGGGACACCATTCTGGATGGCACCCGAGGTGATCCAAAATTCAGATGGATATAATGAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctacagctcttcatctttgactggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
ctttgac putative branch site (score: 4)
tttttttttttatatc putative PPT
atacatattttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atactttgtgcaattaaaaaatcacttggagttctaaattagtactctacagctcttcatctttgactggatacatatttttttttttatatcataacagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTGATGGATATAATGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - tttgtgc
- - - - - - - -aaaaaat
- - - - - - - - - - - cacttgg
- - - - - - - - - - - - - - - - - - - - - - ctctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - ctcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgactg