Sequence
atgc intronic sequence ATGC exonic sequence...gtttccttggtatatatttttttgttctgtcaaggatccacaatttttattcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
Basic information
species | Glycine max |
transcript | GLYMA08G14390.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 1
-----gtttccttggtatatat--ttttttgttctgtcaaggatccacaatttttattcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
||||| | || | | | || | || || || | || || | || |||| || | | || | || | || | | |||||||| ||||| ||||||||| |||||||||||||||| || ||||| ||||||| || || || || ||
gtggaatttcccgcatgcatgtcatatattatgcttgacagaatgtagtatgttagtaatt--tgcttctt-acgccttttgtcacatgtg--tacttgg--tccagGCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTG
upper sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttccttggtat-atatttttttgttctgtcaaggatccacaatttttattcttcct-gctgctagatggctgacaaaatattttgttatctaaatttc---agGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
||| ||| || | | || ||| | || || ||| | | | | | | | | || | ||| | | || || | || ||||| || || ||| | || |||||||||||||| |||||| |||| ||||| |||||||| ||
----tcttattatgatcaagatcgatgatgctaagcactgttgcttctttgctttcttagttagtcattaagcctttatttgtgtt-ctctctgactctctgcagCCTACCATTGGAATCGATTTTCTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG
upper sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------------------------------gtttccttggtatatattt----ttttgttctgtcaaggatccacaatttttattcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
||| | | | || | || | || | | || | || | ||| | | || |||| | | || || | | | || |||||||| ||||| ||||| |||||||||||||||||||||||||| ||||| |||||||| | || || ||
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcatt--gtgttcattggatcaaatt-ctgatatta-gttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
upper sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttccttggtatatatttttttgttctgtcaaggatccacaatttt--tattcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
| ||| ||| | || ||| || | || | || ||||| | | ||| | || | | | | ||||| |||||||| |||||||| || || ||||||||||||||||||||| |||||||||| ||||||| ||
-tagatcatgtagatacaatgctgaa-tgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
upper sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
gtttccttggtatatatttttttgttctgtcaagg-atccacaatttttattcttcctgctgctagatg-gctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
| | ||| ||| | | || || | ||| || | ||| | | | ||| | || | |||| ||||| || ||||| ||||| |||||||| ||||| ||||||||||| ||| |||| |||| |||||||||||
aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaat--tagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
upper sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 2
gtttccttggtatatatttttttgttctgtcaaggatccacaattttt--attcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
| | | || | | | | || | | || | |||||||| | |||| || | ||| | ||| | | || ||||| |||||||| ||||| ||| | ||||||||||||||||||||||| | || || || | ||||||||
-tgttcatgtgcgaaaatctgatgcac-gaaaatattgttcaatttttcaaaacttcgaagtgttctgtggttatggtgataaccaaattttatgtttgcagGCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
atctaaa putative branch site (score: 3)
tgacaaaatattttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttccttggtatatatttttttgttctgtcaaggatccacaatttttattcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- ttccttg
- - - - - - - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - -atccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga