Sequence
atgc intronic sequence ATGC exonic sequencegtacataaaatttctaaaaccttgacatagctagatttgtttttgtttaattaaaataccgtattgacttgtatttatattatttttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
Basic information
species | Glycine max |
transcript | GLYMA06G19320.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G19320.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g36270.1 (Oryza sativa), 3'ss of exon 9
---------gtacataaa-----atttctaaaac-cttgaca-tagctagatttgttttt------gtttaattaaaataccgtatt---gacttgtatttatattattt-ttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
| ||| ||| || || |||| ||||| || |||| |||| | | | | || || | ||| ||| | || | ||||| || || || ||| |||| ||||| ||||||| || || ||||| ||||| | |||||||||||||||||||||||||||||| | |||||| |
gtaaaacttccatataggttcttgtttttatgttgctcgacagtagcttagcttattttgaaaacagtttcctccacaagttctgttcaagaaaccaacgtatgctatatatttgtaaagGTCAAAAGGAGAGGCAAAAGCCATGTTTCTGCGTCACGAGGGTTTTCTAGGAGCACTTGGTGCATTTATGAGTTATGAGAAGCATGGTCTTGATGACTTG
upper sequence: GLYMA06G19320.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G104504_T01 (Zea mays), 3'ss of exon 9
gtacataaaatttctaaaa-----ccttgacatagctagatttgt-ttttgttta-attaaaataccgtattgacttgtatttatattattt---ttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
||| |||| ||| |||| || | | | | || | | || |||| ||||| | || || || || || ||| || | ||||| || || || |||||||| ||||| |||| ||||| || ||||| |||||| | |||||||||||||||||||||||||||||| | |||||| |
gtaaataag--ttccaaaattattccccctcttttatggtttcatatgttatttatattaattttgaaaataatctcgtcccaatgttctttgtgttggtaaagGTCAAAAGGAGAGGCACAAGCTATGTTTCTGCGCCATGAGGGCTTTCTAGGAGCTCTTGGTGCATTTATGAGTTATGAGAAGCATGGTCTTGATGACTTA
upper sequence: GLYMA06G19320.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G32180.3 (Arabidopsis thaliana), 3'ss of exon 9
gtacataaaatttctaaaaccttgacatagctagatttgtttttgtttaattaaaatac-cgtattgacttgtatttatattattt--ttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
||| | | || |||| |||||| |||||| || | | | || | | | | |||| | | | |||| || | ||||||||| || || ||||| ||||||||| | |||||||| |||||||| ||| ||||||| || ||||| ||||||||||| || || ||||| |
gta-acttcacttgtaaa--cttgac----ctagatgtgatat-gcgtactcaccttcttcactcaaacttatttatttattgcttgactacactagGTCTAAGGGAGAGATGCAAGCTATGTTCTTGAGACATGAAGGTTTTCTGGGTGCTCTAGGTGCGTTCATGAGCTATGAGAAGCACGGATTGGATGATTTA
upper sequence: GLYMA06G19320.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g08520.t01 (Vitis vinifera), 3'ss of exon 9
---------------------------------------------------------------------gtacataaa-atttctaaaaccttgacatagctagatttgtt-------tttgtttaattaaaataccgtattgactt--gtatttatatt----atttttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
|| | || | ||| | ||| | | | ||| || ||| || ||| || || |||| | || | | | ||| || |||||||| |||||||| || || |||||||| ||||| ||||||||||| | ||||||||||||||||| ||||| ||||||||||||||| | |||||| |
gtaattgtcaaggaccattattaatttatcaggcttttaagaataaacattcctcagaatgcttgtctagttcctacatgtttttcttctctttgtcctgatcggttttttgccatcattttgttgtttattattttcctttcacttaagagttcaaacttgatattctttgtttagGTCAAATGGGGATGCCCAGGCAATGTTTTTGCGGCATGAAGGATTCTTAGGAGCTTTAGGTGCATTCATGAGCTATGAGAAGCATGGTCTCGATGACTTG
upper sequence: GLYMA06G19320.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ07698 (Selaginella moellendorffii), 3'ss of exon 6
gtacataaaatttctaaaaccttgacatagctagatttgtttttgtttaattaaaataccgtattgacttgtatttatattatttttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
|| | || || || | |||| | | || | | | | ||||| || || ||||| || |||||||||||| | |||||||||||||| || || ||||||||||| |||| || || || || ||| | | ||||
--------------------------------------------gtatgttttcaacactgc-ttgaaattttttaacgtagatcaacgcacagGTCGAAAGGTGAAGCGCAGGCAATGTTCTTGAGGCATGAAGGATTTCTTGGCGCGCTAGGTGCATTTTTGAGCTACGACAAACACGGTCTTGCCAACCTG
upper sequence: GLYMA06G19320.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ07751 (Selaginella moellendorffii), 3'ss of exon 6
gtacataaaatttctaaaaccttgacatagctagatttgtttttgtttaattaaaataccgtattgacttgtatttatattatttttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
|| | || | || | |||| | | || | | | | ||||| || || ||||| || |||||||||||| | |||||||||||||| || || ||||||||||| |||| || || || || ||| | | ||||
--------------------------------------------gtatgttttcgacactgc-ttgaaattttttaacgtagatcaacgcacagGTCGAAAGGTGAAGCGCAGGCAATGTTCTTGAGGCATGAAGGATTTCTTGGCGCGCTAGGTGCATTTTTGAGCTACGACAAACACGGTCTTGCCAACCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgtttaattaaaataccgtattgacttgtatttatattatttttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
tattgac putative branch site (score: 2)
tttttcattt putative PPT
tattgacttgtattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacataaaatttctaaaaccttgacatagctagatttgtttttgtttaattaaaataccgtattgacttgtatttatattatttttcatttagGTCTAATGGGGAAGCACAAGCAATGTTCTTGCGTCATGAAGGATTTCTGGGAGCTTTAGGTGCATTTATGAGTTATGAGAAGCATGGTTTAGATGACCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC