Sequence
atgc intronic sequence ATGC exonic sequence...cttcgaaacctttcatgttgcatcttaatacaagctgttgttaaatatatgttttgattttcttctaatcttcttacattaaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAATCGTGCACGCAACATCCAAAATAAGCCTGTT
Basic information
| species | Glycine max |
| transcript | GLYMA06G04520.1 |
| intron # | 7 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G04520.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g02650.1 (Oryza sativa), 3'ss of exon 7
----cttcgaaacctttcatgttgcatc-ttaatacaagctgttgttaaatatatgttttgattttcttctaatcttcttacattaaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAATCGTGCACGCAACATCCAAAATAAGCCTGTT
| |||| || |||| | | || || | ||||| | | || || ||| | | || | | || | | ||||| | ||||||| || ||||| || ||||| |||||||| ||||| || ||||||||||| ||||| || || || || |||||||| |||||||| ||
ataaataagaaaactcggatgtaccttgattttcactaactgtttt--ggttgatattactattacatgc-aactgacatggatctat--atttttctcctgcagCCTGTATTAGTCCAGCAGATATCAATGCTGAAGAAACACTGAACACTTTGAAATATGCTAACCGCGCTCGTAACATCCAGAATAAGCCAATT
upper sequence: GLYMA06G04520.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G026218_T02 (Zea mays), 3'ss of exon 7
----------------------------------------------------------------cttcgaaacctttcatgttgcatct--taatacaagctgttgttaaatatatgttttgattttcttctaatcttcttacattaaatga---catttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAATCGTGCACGCAACATCCAAAATAAGCCTGTT
|| | | | | || || ||||| | | | || | | | || ||| || | | | | ||||| ||||| | |||| ||||||||||| || |||||||||||||| || || | ||||||||||| ||||| || || ||||| || |||||||| ||||| ||
gtaatttatcttgtcggtgattgctccatgtttcttacattttacttggactatatttgctgatctaagtgatatagaaaattaagtccagtaatatttgtt-taactacaaaaaagtgttgcttgagcttacactcacctgagttaaacatatctttttctcctgcagCTTGCATAAGTCCAGCAGATATTAATGCTGAAGAGACATTAAACACTTTGAAATATGCTAACCGGGCACGTAATATCCAAAACAAGCCGATT
upper sequence: GLYMA06G04520.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g10090.t01 (Vitis vinifera), 3'ss of exon 7
cttcgaaacctttcatgttgcatcttaatacaagctgttgttaaatata-tgttttgattttcttctaatcttcttacatt---aaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAATCGTGCACGCAACATCCAAAATAAGCCTGTT
||| | ||| | |||| || | | || ||| | | | | ||| | || | |||||| ||| |||| | || || || ||||||||| |||||||||||||| |||||||| ||||| || ||||| | ||||||||||||||||| ||||| |||||||||||||| ||
tttcaggattagaaatgct--atctctatgcta-cttttgcaatctgtggcagcaaaactttttcatatttttcttatatttccaaatttc-ttccttttgtagCCTGCATTAGTCCTGCTGATATAAATGCTGAAGAAACTCTGAACACCCTAAAGTATGCAAATCGTGCTCGCAATATCCAAAATAAGCCCGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatgttttgattttcttctaatcttcttacattaaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAATCGTGCACGCAACATCCAAAATAAGCCTGTT
ttcttac putative branch site (score: 2)
tttctatttc putative PPT
ttcttacattaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcgaaacctttcatgttgcatcttaatacaagctgttgttaaatatatgttttgattttcttctaatcttcttacattaaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAATCGTGCACGCAACATCCAAAATAAGCCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - cctttca
- - - - - - - -tgttgca
- - - - - - - - - - - - - - tacaagc
- - - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
