Sequence
atgc intronic sequence ATGC exonic sequence...ctatattgtttatgatgcttgcctagttacctttatacaatatcaattatcttgctagtttactcttttatttgtttatttagaacttgtttcattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG
Basic information
species | Glycine max |
transcript | GLYMA02G39360.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
---ctatattgtttatgatgcttgcctagttacctttatacaatatcaattatcttgctagtt-tactcttttatttgt--------ttatttagaacttgtttcatt--gcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG
| ||||| ||| | | || | || | | | | | | || | || ||| | ||||||||| ||||||| | | || || ||||| ||||| || ||||| || |||||||| |||||||||||||| || || ||||| ||||| || |||||||||||||| ||||||
gtaatgtattggttaagctattt--tgggctagggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 14
ctatattgtttatgatgcttgccta-gttacctttatacaatatcaattatcttgctagtt-tactcttttatttgt--------ttatttagaacttgtttcatt--gcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG
|| || || | | ||| | | || | | | | | | || | || ||| | ||||||||| ||||||| | | || || ||||| ||||| || ||||| || |||||||| |||||||||||||| || || ||||| ||||| || |||||||||||||| ||||||
gtaatttattggttaagctattttgtgctagggtgaaatattctgctttgttctgtgggttgttgatttttatttgcaaaatttattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
ctatattgtt-tatgatgcttgcctagttacctttatacaatatcaattatcttgctagtttactcttttatttg------------tttatttagaacttgtttcattgc-agGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG
|| | ||| | | | || | | | | | ||| ||| ||| || | |||||||| | || ||| || |||| || | | |||| ||||| || ||||| |||||||||| ||||||||||| ||||| || || ||||||||||| || ||||||||||| ||||||
gtaattggttattttaagcaaacttgggc-ttaatgtgaggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 14
ctatattgtttatgatgcttgcctagttacctttatacaatatcaattatcttgctagtttactcttttattt-gtttatttagaacttgtttcattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG
| |||| || | | | | || | | | | | | ||| | || | || || | || || || |||||| || || ||||||||| | ||||||||||||||||| || |||||||| ||||| |||||||||||||| ||||| || ||||||
-tggattgcttgtctcttctcatacactccattcttctgaagttggactccagttgaaatcacttgctgatggaggataattcacattttttggatggcagGGGGCAGTTAATTTTGCTTTAATGATGTCTCAAATGGAAGGAGGTTGCCCAGTTGATTACAACACAATAACAGATCTATTCCTTCAG
upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 15
------ctatattgtttatgatgcttgcctagt--tacctttatacaatatcaattatcttgc-tagtttactcttttatttgtttatttagaac-ttgtttcatt--------gcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG
||| || |||| || || || || | | ||| | || | | | | | ||| || || | | | |||| ||||| ||||||||||||||| |||||||||||||||||||| |||| | || || || || ||||| || || ||||| | || ||||||
gtacttctaaatgacatatgctgtttctttaaaaataacccaaggttgtatttctgataatctacaatctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatcttgctagtttactcttttatttgtttatttagaacttgtttcattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG
cttgtttc CT-rich tract
tagtttactcttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatattgtttatgatgcttgcctagttacctttatacaatatcaattatcttgctagtttactcttttatttgtttatttagaacttgtttcattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG
- - - - - - - - gcttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - cttgcta