Sequence
atgc intronic sequence ATGC exonic sequence...aaaattgacacagtccgaaggagaaaggtgaaggcgtggttataaagatggaggaattattaaacgaaaaaccatttaatcgatgtgtttttacaactagGTCTCCTACGATGTGGAAAAAGCTGTCGGCTTCGGTGGATAAACTATCTTCGTCCTGGCATCAAGCGTGGCCCATTTACTAGTGAAGAAGAAAGTACAAT
Basic information
species | Glycine max |
transcript | GLYMA10G38090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G38090.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00070.t01 (Vitis vinifera), 3'ss of exon 1
aaaattgacacagtccgaagga--gaaaggtgaaggcgtggttata---aagatggaggaattattaaacgaaaaaccatttaatcgatgtgtttttacaact-agGTCTCCTACGATGTGGAAAAAGCTGTCGGCTTCGGTGGATAAACTATCTTCGTCCTGGCATCAAGCGTGGCCCATTTACTAGTGAAGAAGAAAGTACAAT
| | | || || || || | || || | ||| || | | ||||| || || || |||| |||||| || ||||||||||| ||||||||||| ||||||| ||||||||||| || | ||| ||||| || || |||||| |||||||| | | | ||
------gttaggtctctaaagattgatccttggcaacttgtaaatgttcgacgcctgggattttatgattgaaaactttaacgattgaaccaccatttgaacttagGTCTGCTTCGATGTGGAAAGAGCTGTCGGCTGCGGTGGACGAACTATCTTCGCCCAGACATTAAGCGGGGGCCCTTTACTCCGGAAGAAGAGACTGCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatggaggaattattaaacgaaaaaccatttaatcgatgtgtttttacaactagGTCTCCTACGATGTGGAAAAAGCTGTCGGCTTCGGTGGATAAACTATCTTCGTCCTGGCATCAAGCGTGGCCCATTTACTAGTGAAGAAGAAAGTACAAT
atttaat putative branch site (score: 4)
tgttttt putative PPT
aattattaaacgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaattgacacagtccgaaggagaaaggtgaaggcgtggttataaagatggaggaattattaaacgaaaaaccatttaatcgatgtgtttttacaactagGTCTCCTACGATGTGGAAAAAGCTGTCGGCTTCGGTGGATAAACTATCTTCGTCCTGGCATCAAGCGTGGCCCATTTACTAGTGAAGAAGAAAGTACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -tgacaca
- - - - - - - - - - - - - - - - ggcgtgg
- - - - - - - - - - - - - - - - - - - - - - - gatggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattta