Sequence
atgc intronic sequence ATGC exonic sequence...agccataaacatatcaataatttaatttggcattattttttcttgtgtaaagtgatattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
Basic information
species | Glycine max |
transcript | GLYMA06G16720.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g02980.t01 (Vitis vinifera), 3'ss of exon 5
agccataaacatatcaataa-tttaatttggcattattttttcttgtgtaaagtgatattgatttgaataaa-aaatacttacgctat--tcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
| | | | ||| ||| || | | | | || | ||||| | | | ||||| |||| || | ||| ||| |||||| ||||| ||||| |||||||||||||||||||||||||| ||| |||||| | ||||| |||||||| ||||||||||||| ||||| ||||| |
----actagtggttggctcccttttttttaatatatatatatgctccatattattttattggtaatactggttaaataattacacttcggttatcttgatatagGTTAGTCACCACCCTATGATTGTTGCATGCCATTGTGAGGGTCATGGTTGGAAACTATGGGGAGACAGCAACCTAAAAAGTAAATTCTGGGGCCGTTCTA
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------------------------------------------------------agccataaacatatcaataatttaatttggcattattttt--------tcttgtgtaaagtgatattgatttgaataaaaaatacttacgct-attcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
| | | || | | || | | | | | || | || || | | || ||| || | || | ||| |||| |||| || ||||| || |||||||| ||||| || || ||||| || |||||||||||||||||||||||||| || ||||| || |||||||| ||||| |
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
agccataaacatatcaataatttaatttggcattattttt---tcttgtgtaaagtgatattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
| | | || || | |||| ||| ||| || | |||| | | | | | | | | || | | | | | |||| |||||||| || |||||||| ||||| ||||| ||||| || ||||||||||| ||||||||||||||||| ||||| || ||||||||||||||||
--ggagatattaatttgcaacctc-tttgtcatatctttcgagctttagattaagtaaaagttaatcatcttgcatcttctatctccctacgttgctttgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAA
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S427_40V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------agccataaacatat-caataatttaatt-tggcattattttttcttgtgtaaagtgatattgatttgaataaaaaatacttacg-------ctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
|||| | | | | | || ||| | | | ||| | | ||| | | | | || || | || ||| ||| || | | | |||| || |||||||| ||||| || ||||| || || ||||| | || |||||||| ||||| |||||||| || ||||| || |||||||||||||| |
gtttgacgcgattgtcattttctattgtttgacaatctcttaggagtctgatggaattgccacatttgttcgcgccgagatgtttctggtacttgtgcttcatctctaaggaattgtaggttggactgaactataattatctgaaatcctctgttttgcggcgcagGTGAGCCATCACCCAATGATCGTGGCATGTCACTGCGAGGGTCGAGGATGGAAATTCTGGGGAGACAGCAACTTGAAAAGCAAGTTTTGGGGTCGTTCTA
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
agccataaacatatcaataattt-aatttggcattatttt-ttcttgtgtaaagtg-atattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
| ||||||| || | | || | || | | || | || | | || | | || | | | || | || || || | ||||||||||||| || |||||||||||||||||||| ||||| || || |||| ||| |||||||||||||| || ||||| || |||||||| ||||| |
--ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctctacgtgtttttatttttatttttatttttattttgt-acagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 5
agccataaacatatcaataatttaatttggcattattttttcttgtgtaaagtgatattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
||| | || | |||||| | || | |||| |||||| | ||| || | |||||||||| || |||||| | || || || || ||||||||| |||| |||||| | ||||| ||||||||| |||| |||||||||||||| |||||||
--------------------gttagccagtcagtttttttttctctgctacttgatgctgattt-------------------tcttcgtct--gtacagGTCAGTCACCATCCCATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
upper sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
agccataaacatatcaataatttaatttggcattattttttcttgtgtaaagtgatattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
|| || | | || | || ||||| | | ||| || | |||||||||| || || ||| | || || || || ||||||||| |||| |||||| | ||||| ||||||||| |||| |||||||||||||| |||||||
-----------------------------------------gttagctagtcagcttttttctctgctacttgatactgattttcttcgtc--tgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaaagtgatattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
tacttac putative branch site (score: 1)
tgatattgatttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agccataaacatatcaataatttaatttggcattattttttcttgtgtaaagtgatattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
- - - - -catatca
- - - - - - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctattca