Sequence
atgc intronic sequence ATGC exonic sequence...cttcaaaacctttcatgttgcatcttaatacaagcttttgttaaatatatgttttgattttcttctaatcttcttacgtaaaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAACCGTGCACGCAACATAAAAAATAAGCCTGTT
Basic information
species | Glycine max |
transcript | GLYMA04G04380.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G04380.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g02650.1 (Oryza sativa), 3'ss of exon 7
--cttcaaaacctttcatgttgcatcttaatacaagcttttgttaaatatatgttttgattttcttctaatct---tcttacgtaaaatgacatt--tctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAACCGTGCACGCAACATAAAAAATAAGCCTGTT
|| | || | || | ||| || ||| ||| | | | ||||| || | | | | || || | | | ||| ||| | ||||||| || ||||| || ||||| |||||||| ||||| || ||||||||||| ||||| ||||| || || ||||| | |||||||| ||
ataaataagaaaactcg-gatgtaccttgat------tttcactaactgttttggttgatattactattacatgcaactgacatggatctatatttttctcctgcagCCTGTATTAGTCCAGCAGATATCAATGCTGAAGAAACACTGAACACTTTGAAATATGCTAACCGCGCTCGTAACATCCAGAATAAGCCAATT
upper sequence: GLYMA04G04380.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G026218_T02 (Zea mays), 3'ss of exon 7
----------------------------------------------------------------cttcaaaacctttcatgttgcatct--taatacaagcttttgttaaatatatgttttgatttt-cttctaatcttcttacgtaaa-atgacattt-ctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAACCGTGCACGCAACATAAAAAATAAGCCTGTT
|| | | | || || ||||| | ||| || | | | || ||| || ||| | || || | |||| || | ||| || | |||| ||||||||||| || |||||||||||||| || || | ||||||||||| ||||| ||||| ||||| || || |||| ||||| ||
gtaatttatcttgtcggtgattgctccatgtttcttacattttacttggactatatttgctgatctaagtgatatagaaaattaagtccagtaatatttg-tttaactacaaaaaagtgttgcttgagcttacactcacctgagttaaacatatctttttctcctgcagCTTGCATAAGTCCAGCAGATATTAATGCTGAAGAGACATTAAACACTTTGAAATATGCTAACCGGGCACGTAATATCCAAAACAAGCCGATT
upper sequence: GLYMA04G04380.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g10090.t01 (Vitis vinifera), 3'ss of exon 7
cttcaaaacctttcatgttgcatcttaatacaagcttttgttaaatata-tgttttgattttcttctaatcttcttacgta---aaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAACCGTGCACGCAACATAAAAAATAAGCCTGTT
|||| | ||| | |||| || | | |||||| | | | | ||| | || | |||||| | |||| | || || || ||||||||| |||||||||||||| |||||||| ||||| || ||||| | ||||||||||| ||||| ||||| || |||||||||| ||
tttcaggattagaaatgct--atctctatgcta-cttttgcaatctgtggcagcaaaactttttcatatttttcttatatttccaaatttc-ttccttttgtagCCTGCATTAGTCCTGCTGATATAAATGCTGAAGAAACTCTGAACACCCTAAAGTATGCAAATCGTGCTCGCAATATCCAAAATAAGCCCGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatgttttgattttcttctaatcttcttacgtaaaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAACCGTGCACGCAACATAAAAAATAAGCCTGTT
ttcttac putative branch site (score: 2)
tttctatttc putative PPT
ttttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcaaaacctttcatgttgcatcttaatacaagcttttgttaaatatatgttttgattttcttctaatcttcttacgtaaaatgacatttctatttcagCCTGCATAAGTCCTGCTGATATTAATGCTGAGGAAACCCTTAACACTTTGAAGTATGCAAACCGTGCACGCAACATAAAAAATAAGCCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- -caaaacc
- - - - - - - -tgttgca
- - - - - - - - - - - - - - tacaagc
- - - - - - - - - - - - - - - - - - - - - - - - -tgttttg