Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtgtggctgttaaaaactatgaatatggatattttgtaggatagttctttaaattgtttgatctaaaggtttttgtttccttttatttccattacagCATCACCATACTTTTCTTTGCAAAAGAAGGGGAAGGTTGCACACTAACTCCAATGAAAGAAAATGTTCTTCCACCCGTGACTGTAAATTTCCAGCAAGGA
Basic information
species | Glycine max |
transcript | GLYMA13G20270.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20270.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g01940.t01 (Vitis vinifera), 3'ss of exon 1
-----tgtgtgtggctgttaaaaactatgaatatggatattttgtaggatagttctttaaattgtttgatctaaaggtttttgtttccttttatttccattacagCATCACCATACTTTTCTTTGCAAAAGAAGGGGAAGGTTGCACACTAACTCCAATGAAAGAAAATGTTCTTCCACCCGTGACTGTAAATTTCCAGCAAGGA---
|| | | || | | | | | | ||| || ||| | || | | || | | |||| |||||||||||| || | || ||||||||||||| ||||||||||||||||||| |||| || | || | |||||||| ||||| || ||| || |||||| ||||||| || ||
tttgaagtttccatccttttgatggc-tcactgttgtctatttttaaaatatattttca---tattcgttttaaaaatttttgtttcctacaatctgcaa-acagCATCACCATTATTTTCTTTGCAAAAGAAGGCGAAGACTGTAGCCTGTCGCCAATGAAGGAAAAC---CTGGAACCAGTCACTGTACATTTCCAACAGGGTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttctttaaattgtttgatctaaaggtttttgtttccttttatttccattacagCATCACCATACTTTTCTTTGCAAAAGAAGGGGAAGGTTGCACACTAACTCCAATGAAAGAAAATGTTCTTCCACCCGTGACTGTAAATTTCCAGCAAGGA
atctaaa putative branch site (score: 3)
tttttgtttcctttta putative PPT
tttaaattgtttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtgtggctgttaaaaactatgaatatggatattttgtaggatagttctttaaattgtttgatctaaaggtttttgtttccttttatttccattacagCATCACCATACTTTTCTTTGCAAAAGAAGGGGAAGGTTGCACACTAACTCCAATGAAAGAAAATGTTCTTCCACCCGTGACTGTAAATTTCCAGCAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
-gtgtgtg
- - - - gctgtta
- - - - - - - - - -ctatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttg