Sequence
atgc intronic sequence ATGC exonic sequencegtaagcattgagattgctaattttctttttatacttggttgtattgaattagtacacctagttgataattgaaaatttgaaactttatatctgtgatttgtttattatattgggcagATTCATGGACAAGGCAGCAACAATTAAAGAGACTGAGGAGCATAGTCCAAAGAATCCATGGAGGCTCTGCACTGTGACTCAAGTGGAGGAAGCCAAATGT
Basic information
species | Glycine max |
transcript | GLYMA20G39150.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G39150.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g01300.t01 (Vitis vinifera), 3'ss of exon 3
gtaagca-ttgagattgctaatttt-ctttttatacttggttgtattgaattagtacacctagttgataattgaaaatttgaaac-tttatatctgtgatttg------tttattatattgggcagATTCATGGACAAGGCAGCAACAATTAAAGAGACTGAGGAGCATAGTCCAAAGAATCCATGGAGGCTCTGCACTGTGACTCAAGTGGAGGAAGCCAAATGT---
||||| | ||| ||||| |||| |||||| || || | | || | | || | || ||||||| | ||| |||| | || | | |||||| ||| ||| | |||||||| || || || | |||| | || | || || ||||||||| || ||||||||||||||||| || ||||||||||||
gtaagtagttgtttttgcttttttttcttttttctttttcttcttcttcttttttttttttttttttttgttaaaaatttattatattttcatctatttattaacaacatccttgatattgatcagGTTCCTAGACAAGGCCGCCACGATGATAGAGGCCGATATGGTGGACCCTAA---TCCATGGAGACTTTGCACTGTGACTCAAGTTGAAGAAGCCAAATGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgataattgaaaatttgaaactttatatctgtgatttgtttattatattgggcagATTCATGGACAAGGCAGCAACAATTAAAGAGACTGAGGAGCATAGTCCAAAGAATCCATGGAGGCTCTGCACTGTGACTCAAGTGGAGGAAGCCAAATGT
agttgat putative branch site (score: 5)
tttatatctgtgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcattgagattgctaattttctttttatacttggttgtattgaattagtacacctagttgataattgaaaatttgaaactttatatctgtgatttgtttattatattgggcagATTCATGGACAAGGCAGCAACAATTAAAGAGACTGAGGAGCATAGTCCAAAGAATCCATGGAGGCTCTGCACTGTGACTCAAGTGGAGGAAGCCAAATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA