Sequence
atgc intronic sequence ATGC exonic sequencegtcaatattgattaaaatttatgctcctgcagctagctataatctcttcttttcactcacccaactcttggaagctttcagATTGACAGGAAACTGGTCAAACAGACAGTGATGACTTCAGTTTATGGTGTTACCTTTGTTGGGGCACGAGAGCAAATCAAGAGAAGATTAGAGGAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA17G07940.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G07940.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G24120.2 (Arabidopsis thaliana), 3'ss of exon 12
gtcaatattga----ttaaaatttatgctcctgcagctagctataatctcttcttttcactcacccaactcttggaagctttcagATTGACAGGAAACTGGTCAAACAGACAGTGATGACTTCAGTTTATGGTGTTACCTTTGTTGGGGCACGAGAGCAAATCAAGAGAAGATTAGAGGAGAAAG
|| | ||| | || ||| | | ||| | ||| | | | | | | | || |||| || |||||| | |||||||| ||||| || ||||| || ||||| ||||| |||||||| |||| ||| ||||| || || ||||| || ||||||||||| |||||||
gtgagtatcaacggtttttgattgaacattatgccac-agcaaaagttcttcccagtgatgcaatgttttcttctaa--tttcagGTCGACAGGAAGCTGGTAAAGCAGACGGTAATGACGTCAGTATATGGTGTCACCTATGTAGGGGCTCGTGAACAAATAAAAAGAAGATTAGAAGAGAAAG
upper sequence: GLYMA17G07940.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 12
------------------------------------------gtcaatattgattaaaatttatgctcctgcagctagctataatctcttcttttcactcaccc---------------aactcttggaagctttcagATTGACAGGAAACTGGTCAAACAGACAGTGATGACTTCAGTTTATGGTGTTACCTTTGTTGGGGCACGAGAGCAAATCAAGAGAAGATTAGAGGAGAAAG
|||| |||||| | || || | | | | | | | | | ||||||| | | | | | | | |||||||||| | || ||||| | || |||||||||||||||||||| || ||||||||||||| | |||| ||||| ||||||||||| |||||||| | |||||| |
gttggttatcctatgttattctggagtcccatatcacaccttgtcattattgaatgaacattttagttaataacttgacagttttttttccttttcaatttctctccattgatgattaaaggtttggtaagctttcagGTGGATCGGAAATTAGTAAAACAGACAGTGATGACTTCTGTGTATGGTGTTACCTATATTGGTGCACGTGAGCAAATCAAAAGAAGATTGGCGGAGAAGG
upper sequence: GLYMA17G07940.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------------------gtcaa-tattgat--taaaatttatgctcctgcagctagctataatctcttcttttcactcacccaactcttggaagcttt-----cagATTGACAGGAAACTGGTCAAACAGACAGTGATGACTTCAGTTTATGGTGTTACCTTTGTTGGGGCACGAGAGCAAATCAAGAGAAGATTAGAGGAGAAAG
| ||| | || | ||| ||||| |||| | || | ||| | |||| | | ||| | | | ||||||| || || || ||||| |||||||||||||| ||||| ||||| ||||| |||||||| || || |||||| | ||||| ||||| |
gtatgaaccgaacgactactcattttgttgttactgctatgccaagtgttaaaagtaatatttaggctcttttttctggacatactgcaggttttttgtggtactgatctttgcatattctatgtgtagATTGATAGAAAGCTTGTCAAGCAGACAGTGATGACATCAGTGTATGGAGTTACTTTTGTTGGCGCCCGCATGCAAATATTTAATAGATTGAAGGAGCGTG
upper sequence: GLYMA17G07940.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ20792 (Selaginella moellendorffii), 3'ss of exon 12
gtcaatattgattaaaatttatgctcctgcagctagctataatctcttcttttcactcacccaactcttggaagctttcagATTGACAGGAAACTGGTCAAACAGACAGTGATGACTTCAGTTTATGGTGTTACCTTTGTTGGGGCACGAGAGCAAATCAAGAGAAGATTAGAGGAGAAAG
| || | || || ||| || | || | || | | ||| | || |||||||| || |||||||||||||||||||| ||||| || || || | ||||| ||||| | ||||| | | ||| | ||| || |
----------------------------gtgagtatccatttcggttttctttacctttctcatcaattcttcggtcacagGTGGATAGGAAACTAGTGAAACAGACAGTGATGACTTCGGTTTACGGCGTGACATACGTTGGAGCACGTAACCAAATAACAAACAGACTTAGGGACAAGG
upper sequence: GLYMA17G07940.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ32457 (Selaginella moellendorffii), 3'ss of exon 12
gtcaatattgattaaaatttatgctcctgcagctagctataatctcttcttttcactcacccaactcttggaagctttcagATTGACAGGAAACTGGTCAAACAGACAGTGATGACTTCAGTTTATGGTGTTACCTTTGTTGGGGCACGAGAGCAAATCAAGAGAAGATTAGAGGAGAAAG
| | | | | | |||| || |||| | || |||| | | ||| | || |||||||| || |||||||||||||||||||| ||||| || || || | ||||| ||||| | ||||| | | ||| | ||| || |
------------------------gtgagtatccatttcggttttctttacttttctcatc-aattcttcgg---tcacagGTGGATAGGAAACTAGTGAAACAGACAGTGATGACTTCGGTTTACGGCGTGACATACGTTGGAGCACGTAACCAAATAACAAACAGACTTAGGGACAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcagctagctataatctcttcttttcactcacccaactcttggaagctttcagATTGACAGGAAACTGGTCAAACAGACAGTGATGACTTCAGTTTATGGTGTTACCTTTGTTGGGGCACGAGAGCAAATCAAGAGAAGATTAGAGGAGAAAG
cactcac putative branch site (score: 2)
ctttc putative PPT
tataatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaatattgattaaaatttatgctcctgcagctagctataatctcttcttttcactcacccaactcttggaagctttcagATTGACAGGAAACTGGTCAAACAGACAGTGATGACTTCAGTTTATGGTGTTACCTTTGTTGGGGCACGAGAGCAAATCAAGAGAAGATTAGAGGAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA