Sequence
atgc intronic sequence ATGC exonic sequence...aactgaataagggggggcccgtattgggaattcttgggcatttggtctttaatgtttctgttaccataaaatatatttattgacagcttcactatggcagAATCTGAAGTCAAACCTGACAATGTGGAAGCTTGGAACCCTTCCTCCTGCTTTAATTGCATTTAAAGGACTTGTTCACCCAATTGATCCCTCTTGGCACA
Basic information
species | Glycine max |
transcript | GLYMA18G49960.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G49960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G098434_T01 (Zea mays), 3'ss of exon 5
aactgaataagggggggcccgtattgggaattcttgggcatttggtctttaatgtttctgttaccataaaatatatttat-tgacagcttcactatg-gcagAATCTGAAGTCAAACCTGACAATGTGGAAGCTTGGAACCCTTCCTCCTGCTTTAATTGCATTTAAAGGACTTGTTCACCCAATTGATCCCTCTTGGCACA
| | || | |||| ||| | | || || || | ||| | | || || | | | | | |||||| |||||||||||| | ||| | |||| ||| ||||| | || || | | || ||||||||||| | |||||||||||||||||| || |||||
-tcagcattactttccagtttaattgattattgaaactctctgcagtcttcat-ttgatagtacaaaatgatgagcttccattcttgttcctttgcatgcagAACCTGAAGTCAAACTTCACACTTTGGAGGCTGGGAACATTACCACCAGGCCTTATAGCATTTAAAGGCCATGTTCACCCAATTGATCCATCATGGCATC
upper sequence: GLYMA18G49960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G01040.2 (Arabidopsis thaliana), 3'ss of exon 5
aactgaataa-gggggggcccgtattgggaattcttgggcatttggtctttaatgtttctgttaccataaaatatatttattgaca--gcttcactatggcagAATCTGAAGTCAAACCTGACAATGTGGAAGCTTGGAACCCTTCCTCCTGCTTTAATTGCATTTAAAGGACTTGTTCACCCAATTGATCCCTCTTGGCACA
| || | | ||| ||| || | ||| | || | | ||| ||| | || ||| || |||| | || |||||||||||||| || || ||||||||||| |||||||| | ||||||||| |||| ||||||||||| | |||||| ||||| ||| |||||||||| |
-gtaaagtatcagagaagcctgtaatg-----ttttgagttttagattcgaaattggcaaattatt---gatcatgcttactggttttgctttgatgtg-cagAATCTGAAGTCGAATCTAACAATGTGGAAACTTGGAACATTGCCTCCTGCTCTAATAGCATTTAAAGGTCATGTTCAGCCAATAGATTCCTCTTGGCATA
upper sequence: GLYMA18G49960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G15470.1 (Arabidopsis thaliana), 3'ss of exon 5
--aactgaataagggggg---gcccgtattgggaattcttgggcatttggtctttaatgtttctgttaccataaaatatatttattgacagcttcactatggcagAATCTGAAGTCAAACCTGACAATGTGGAAGCTTGGAACCCTTCCTCCTGCTTTAATTGCATTTAAAGGACTTGTTCACCCAATTGATCCCTCTTGGCACA
|||| || | | | | || | ||||| ||| | | ||| ||| | | || | | | |||| | | | | |||||||| |||||||| |||||||||||||| ||||||||| | ||||||||| | || || || || || | || ||| ||| || | || ||||| |
gtaactctatcgaataagcttacacttttttgtttttctttagca----gAATCTAAAGTTACCTCTCTAATCTACTCTGTTTACTT----TTGCTTTGGAACAGAATCTAAAGTCAAATCTGACAATGTGGAAACTTGGAACCTTGCCTCCTGCTCTTATCGCGTTCAAGGGTCACGTACACATAATAGACTCGTCATGGCATA
upper sequence: GLYMA18G49960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0108g01520.t01 (Vitis vinifera), 3'ss of exon 5
-aactgaataagggggggcccgtattgggaattcttgggcatttggtctttaatgtttct-gttaccataaaatatatttattg-acagcttcactatggcagAATCTGAAGTCAAACCTGACAATGTGGAAGCTTGGAACCCTTCCTCCTGCTTTAATTGCATTTAAAGGACTTGTTCACCCAATTGATCCCTCTTGGCACA
| ||| | | ||| | |||| || |||| | || ||||| || | |||| || | || | | |||||||||||||||||||||| |||||||||||||||||||| ||||||||||| || ||||||||||| | | |||||||||| || || || |||||||
tgagcttttaattgattatatattttgtttaaatgataaaattt---ctgggatgtgcttagtcaccatttcttacttggattgtggggcctttctgttgtagAATCTGAAGTCAAACCTGACTATGTGGAAGCTTGGAACCCTACCTCCTGCTTTGATAGCATTTAAAGGTCATATTCACCCAATCGACCCATCCTGGCACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttaatgtttctgttaccataaaatatatttattgacagcttcactatggcagAATCTGAAGTCAAACCTGACAATGTGGAAGCTTGGAACCCTTCCTCCTGCTTTAATTGCATTTAAAGGACTTGTTCACCCAATTGATCCCTCTTGGCACA
tattgac putative branch site (score: 2)
cttcact putative PPT
tttctgttaccataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aactgaataagggggggcccgtattgggaattcttgggcatttggtctttaatgtttctgttaccataaaatatatttattgacagcttcactatggcagAATCTGAAGTCAAACCTGACAATGTGGAAGCTTGGAACCCTTCCTCCTGCTTTAATTGCATTTAAAGGACTTGTTCACCCAATTGATCCCTCTTGGCACA
- - - - - ggggggg
- - - - - - - - - - - - - - - - - - -gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcttc