Sequence
atgc intronic sequence ATGC exonic sequence...cctcaaacatttcacaacctctagtctcttcaataattgggataatatttttttctttttacccttattactaatattaactgcatttctcttttggcagGTAAAGCGATGTGGAGAAATGTCAAGAAAGCTACGATTCTTCAAGGATCAAATCAGTAAAGCTGGTCTAATGTCTTCTTCTCGTACTGAATTGCAACCCG
Basic information
species | Glycine max |
transcript | GLYMA13G40430.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G40430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g03450.t01 (Vitis vinifera), 3'ss of exon 2
cctcaaacatttcacaacctctagtctcttcaataattgggataatatttttttcttt-ttacccttattactaatattaac--tgcatttctcttttggcagGTAAAGCGATGTGGAGAAATGTCAAGAAAGCTACGATTCTTCAAGGATCAAATCAGTAAAGCTGGTCTAATGTCTTCTTCTCGTACTGAATTGCAACCCG
| ||| | | | ||| || || ||||||| || || | ||| | | | ||| || | |||| | || | ||| |||||||| ||||||||||| ||| |||||||||||||||| ||||| |||||| |||||||||||||| |||| |||||| ||||| |||| ||||||| |
-tatggatgttttatc-tttattgtccttttcttagttgggatgatgttataacatttactgcttattttagtagttttaatatttcagagatatttcc-cagGTAAAACGATGTGGAGAGATGGCAAGAAAGCTACGATTTTTCAAAGATCAAGTCAGTAAAGCTGGTTTAATCTCTTCTGCTCGTCCTGATCTGCAACCAG
upper sequence: GLYMA13G40430.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S107_75V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------cctcaaacatttcacaacctctagtctcttcaataattgggataatatttttttctttttacccttattactaatattaac-tgcatttctcttttggcagGTAAAGCGATGTGGAGAAATGTCAAGAAAGCTACGATTCTTCAAGGATCAAATCAGTAAAGCTGGTCTAATGTCTTCTTCTCGTACT--GAATTGCAACCCG
| || |||| ||| || | ||| || | ||| | | | |||| || ||| | | | ||||| ||||||||||||||||||||||||||| |||| | ||| |||| ||||| | ||| ||||| || || | | | || || |||
gtgcgttctccgacatccttctatgttcctttttggttatttttggttaggtgtttgttggttgtgttttttctattcttagtcgagcttaattttatacacttcacactttgtgaatgtcgaacgtggtaacctggttttgtatactctcagGTTAAGCGATGTGGAGAAATGTCAAGAAAGATACGTTACTTTCAGGACCAAATTACAAAATCTGGTAGAACAGCTGCATACAGGCCTTTGAGGGACAAAG--
upper sequence: GLYMA13G40430.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S60_200V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------cctcaaacatttcacaacctctagtctcttcaataa------ttgggataatattttttt---ctttttaccctt-----attactaatattaactgcatttctcttttggcagGTAAAGCGATGTGGAGAAATGTCAAGAAAGCTACGATTCTTCAAGGATCAAATCAGTAAAGCTGGTCTAATGTCTTCTTCTCGTACTGAATTGCAACCCG--
| | ||| | || | | || | || || |||| ||| |||| || ||| | | | | || | | | | || |||| |||||||||||||| ||| ||||||||||||||| || | || ||||| ||||||||||| || || | | | || | | |
gtgaggattctcgacacctctgaaaatgtttgttaggaattcgttgatttccctttccctcgtacactttcctttgggctgcatttccccacccttgataccttttgcatgttagttttttaacctcaagatgtgtgttattagGTGAAGCGATGTGGAGAGATGGCAAGAAAGCTACGATATTTTCACGACCAAATTGCTAAAGCTGGTCAAACACCTGCACAGAGACCC--ATGGTAGACAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttttttctttttacccttattactaatattaactgcatttctcttttggcagGTAAAGCGATGTGGAGAAATGTCAAGAAAGCTACGATTCTTCAAGGATCAAATCAGTAAAGCTGGTCTAATGTCTTCTTCTCGTACTGAATTGCAACCCG
tattaac putative branch site (score: 1)
ctgcatttctctttt CT-rich tract
ttattactaatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctcaaacatttcacaacctctagtctcttcaataattgggataatatttttttctttttacccttattactaatattaactgcatttctcttttggcagGTAAAGCGATGTGGAGAAATGTCAAGAAAGCTACGATTCTTCAAGGATCAAATCAGTAAAGCTGGTCTAATGTCTTCTTCTCGTACTGAATTGCAACCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- -caaacat
- - - - - - cacaacc
- - - - - - - - - - - - -ctcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttc