Sequence
atgc intronic sequence ATGC exonic sequence...aacattcttaatttttacattgtgctttcatgtggaattttagttgaaaaaatcaggccagggtttatttaatttttttttaacgttttaaccgtttcagGAAGAAGGCTGGGTTGTGTGTAGAGTGTTCAAGAAGAGAATGACAACAATGCAGAAAGTGGGAGAGTATGATCAATCACCCTGTTGGTACGATGAGCAAG
Basic information
species | Glycine max |
transcript | GLYMA17G14700.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G14700.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------aacatt--cttaatttttacattgtgctttcatgtggaattttagttgaaaaaatcagg-ccagggtttatttaat----ttttttttaacgttttaaccgtttcagGAAGAAGGCTGGGTTGTGTGTAGAGTGTTCAAGAAGAGAATGACAACAATGCAGAAAGTGGGAGAGTATGATCAATCACCCT---GTTGGTACGATGAGCAAG
|| || | || |||| | | | || | || |||||| | | || | || | |||| | | | || || | | | ||| |||||||||| |||||||||||||| || |||||||||||| || | || | | ||||||| || || ||| || | |||||||||||| |
gtattaatataacaaccctaaaacattacttctctataaaagttagttgcatgtttatactaaacaatctcattatatgatagttgcatatatgatctcctaaaatcatttgaggtaatctcattaaatgatatttgggttgtagGAAGAAGGATGGGTTGTGTGTAGGGTTTTCAAGAAGAGATTGGCTGCAGTTAGACGAATGGGAGATTACGACTCATCCCCTTCACATTGGTACGATGATC---
upper sequence: GLYMA17G14700.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 2
aacattcttaatttttacattgtgctttcatgtggaattttagttgaaaaaatcaggccagggtttatttaatttttttttaacgttttaaccgtttcagGAAGAAGGCTGGGTTGTGTGTAGAGTGTTCAAGAAGAGAATGACAACAATGCAGAAAGTGGGAGAGTATGATCAATCACCCTGTTGGTACGATGAGCAAG-------
||| | | ||| | || | | | | | | || | | | | ||||| | || | || | |||||||||||| ||||| || ||||| || ||||||||||||||| ||||||||| ||||||||| || ||| ||||| |||||||| ||||| ||||
-ctattttatgtgtttgccttccaatctta---gtgctcacaattcttttagtttgatatgaagttattgtgcctgaagatattactgcaattgcatcaggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCAACAATGCGGAAAGTGGGTGAACATGG---GTCACCATGTTGGTATGATGACCAAGTTTCATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaaaatcaggccagggtttatttaatttttttttaacgttttaaccgtttcagGAAGAAGGCTGGGTTGTGTGTAGAGTGTTCAAGAAGAGAATGACAACAATGCAGAAAGTGGGAGAGTATGATCAATCACCCTGTTGGTACGATGAGCAAG
ttttaac putative branch site (score: 2)
ccgtttc CT-rich tract
tttatttaattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacattcttaatttttacattgtgctttcatgtggaattttagttgaaaaaatcaggccagggtttatttaatttttttttaacgttttaaccgtttcagGAAGAAGGCTGGGTTGTGTGTAGAGTGTTCAAGAAGAGAATGACAACAATGCAGAAAGTGGGAGAGTATGATCAATCACCCTGTTGGTACGATGAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - tcaggcc