Sequence
atgc intronic sequence ATGC exonic sequencegtcagaataatgcatgttgaatgtaccatacctaaacatgatggcacgttgcaatcttatgttgggttcagGGTTCAACATGATAATGGCACAGGCCCCATGAAAGGAGGAATCAGATACCATCCTGAG
Basic information
species | Glycine max |
transcript | GLYMA11G16320.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G16320.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------gtcagaataatgcatgttgaatgtaccatacctaaacatgatggcacgttgcaatcttatgttgggttcagGGTTCAACATGATAATGGCACAGGCCCCATGAAAGGAGGAATCAGATACCATCCTGAG
|| | |||| |||||||| || || || ||| ||||||| || ||| ||| |||||||| || ||||||||||||||||||| | || || ||||| || |||||||
acttaaccaggatcagtattttataaggttcatctgggctttcccccctatccgaaacagtatgttcaacttttgagtaacaagcagtttgtg-gttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA--------------
upper sequence: GLYMA11G16320.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------------------------------------gtcagaataa---tgcatgttgaatgtaccatacctaaacatgatggcacgttgcaatcttatgttgggttcagGGTTCAACATGATAATGGCACAGGCCCCATGAAAGGAGGAATCAGATACCATCCTGAG
| ||| || |||| ||||| || |||||||| ||| | ||||| || ||| ||| | |||||| ||||||||||||||||| |||| | |||||||||||| ||||| ||||
gtggtttctaatgatatgctcagttttctcatccatgataaccgtatgatttaccattttttgactatgctcttttcacttcttttgaacaaaattgcagGTTGAGTGCACCATACCCAAAGACGATGGTACTTTGGCATCATTTGTTGGATTCAGGGTTCAACATGACAATGCTAGAGGCCCCATGAAGGGAGGGATCA-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaatgtaccatacctaaacatgatggcacgttgcaatcttatgttgggttcagGGTTCAACATGATAATGGCACAGGCCCCATGAAAGGAGGAATCAGATACCATCCTGAG
acctaaa putative branch site (score: 3)
aatcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagaataatgcatgttgaatgtaccatacctaaacatgatggcacgttgcaatcttatgttgggttcagGGTTCAACATGATAATGGCACAGGCCCCATGAAAGGAGGAATCAGATACCATCCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA