Sequence
atgc intronic sequence ATGC exonic sequence...aatctcccaatcttttttttttctttcaattatcaaatcaatgttataatcccattttttttttctaatttggtgttcatttttgtgtgtgtggggctagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGGAGAAGGAGTTTGCTCTACAGCCTCTTGATGCCAGTGATGTCC
Basic information
species | Glycine max |
transcript | GLYMA12G17510.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G17510.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
aatctcccaatcttttttttttctttcaattatcaaatcaatgttataatcccattttttttttctaatttggtgttca----tttttgtgtgtgtggggct----agTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGGAGAAGGAGTTTGCTCTACAGCCTCTTGATGCCAGTGATGTCC
|| ||||| || | | | | | |||||| | || | ||| || || ||| | | | ||| | | || ||||||||||| || || ||||||||||| ||||||||||| ||||| ||||||| || || | |||||||| ||||||||||| |||||| |
--------gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
upper sequence: GLYMA12G17510.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G54510.1 (Arabidopsis thaliana), 3'ss of exon 1
aatctcccaatcttttttttttctttcaattatcaaatcaatgtt--ataatcccattttttttttcta---atttggtgttcatttttgtgtgtgtggggctagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGGAGAAGGAGTTTGCTCTACAGCCTCTTGATGCCAGTGATGTCC
||| || | || | || | | || ||| || || | | |||| | || | ||| | || | | | || ||||||||||| || || || |||||||| |||||||||||||| ||||| || |||| ||||| | |||||||| ||||||||||| |||||| |
-----tccattcactgttaaaacctttatccaaaaagaaaatttttaatgggtctacttttatctttcatatattcacaaaagaattattgatatatgtcaacagTTCTGGGACTTCTGGTGGAGAGAGGAAACTGATGCCAACAATCGAAGAGGAACTAGACAGAAGATCACTTCTCTACAGTCTCTTGATGCCTGTGATGGAC
upper sequence: GLYMA12G17510.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0014g04690.t01 (Vitis vinifera), 3'ss of exon 1
-aatctcccaatcttttttttttctttcaattatcaaatcaatgttataatcccattttttttttctaatttggtgttcatttttgtgtgtgtggggct--agTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGGAGAAGGAGTTTGCTCTACAGCCTCTTGATGCCAGTGATGTCC
|| | | || | || | | | | || || || || || | | | ||| ||||| | || | | | || || ||||| || || || |||||||||||||||||||| || ||||||||||| | ||| ||| ||||| || || || | ||||| |||||| |
gtattgttcgttgttggtaattggggtgagaggcttttcagaatgtgtactcaaatggattgaaactgaat-gcggttgctttttatttgctttgctttgcagCTCGGGGACTTCTGGCGGGGAGAGGAAGCTGATGCCAACCATAGAAGAAGAGCTGGAGAGGAGGTCATTGCTTTATAGTCTGCTCATGCCGGTGATGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatcccattttttttttctaatttggtgttcatttttgtgtgtgtggggctagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGGAGAAGGAGTTTGCTCTACAGCCTCTTGATGCCAGTGATGTCC
ttctaat putative branch site (score: 2)
attttttttttctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatctcccaatcttttttttttctttcaattatcaaatcaatgttataatcccattttttttttctaatttggtgttcatttttgtgtgtgtggggctagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGGAGAAGGAGTTTGCTCTACAGCCTCTTGATGCCAGTGATGTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- tctccca
- - - - - - - - - - - - - - - - - - - caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgt