Sequence
atgc intronic sequence ATGC exonic sequence...gtttgacagcactaatatgcggcatgcattcaaaatcttatagcttaggtgtactcatttatgtttgatggaaggtatacattgacttttactttttcagAACCTCAGAACTTGTGGAAGCAGTTCTGCAAGGGAGGAATGGATCAGTTTTCTGTTATGGTGCCACCGGAGCTGGAAAAACTTATACAATGCTTGGTACA
Basic information
species | Glycine max |
transcript | GLYMA18G22930.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G22930.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g42070.1 (Oryza sativa), 3'ss of exon 1
gtttgacagcactaatatgcggcatgcattcaaaatcttatagcttaggtgtact-catttat-gtttgatggaaggtatacattgacttttactttttcagAACCTCAGAACTTGTGGAAGCAGTTCTGCAAGGGAGGAATGGATCAGTTTTCTGTTATGGTGCCACCGGAGCTGGAAAAACTTATACAATGCTTGGTACA
||| | | || | | | || | || ||| | | | ||| ||| | || | | ||| ||| |||| | | | |||||| ||||| |||||||| | ||||||||||| |||||||| | || ||||| ||||| ||||| || ||||| || || || ||||||||||| ||
tcatgagaaagtgtactagccttgttcgattgcgat-tcatcgctaaaatccggtacatatatagcatggagttaattatccatcttctttga-tgctgcagAACATCAGATCTTGTGGAGGGTGTTCTGCAAGGTAGGAATGGGACGGTGTTCTGCTATGGAGCCACTGGTGCTGGGAAGACCTACACAATGCTTGGGACG
upper sequence: GLYMA18G22930.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G18550.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttgacagcactaatatgcggcatgcattcaaaat--cttatagcttaggtgtactcatttatgtttgatggaaggtatacattgacttttactttttcagAACCTCAGAACTTGTGGAAGCAGTTCTGCAAGGGAGGAATGGATCAGTTTTCTGTTATGGTGCCACCGGAGCTGGAAAAACTTATACAATGCTTGGTACA
|| | | || || || | | ||| | | | | | | ||| || | | || | | | ||| | || |||||||| ||| ||||| ||||||||||| |||| || ||||| ||||||||||| || ||||| || ||||| || || |||||||| ||| | || |||
--------------gtaagtgtaattcaaccatattgccttgaataatggatcttttgattagcatt-gttcttagatgtctttcccttttgatttattcagAACAGGAGATCTTGTTGAAGCAGTTCTTGAAGGAAGAAATGGTTCAGTTTTCTGCTACGGTGCTACGGGAGCAGGCAAGACTTATACGATGTTAGGGACA
upper sequence: GLYMA18G22930.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g04330.t01 (Vitis vinifera), 3'ss of exon 1
gtttgacagcactaatatgcggcatgcattcaaaatctta-tagcttaggtgt-actcatttatgtttga-tggaaggtatacattgac-ttttactttttcagAACCTCAGAACTTGTGGAAGCAGTTCTGCAAGGGAGGAATGGATCAGTTTTCTGTTATGGTGCCACCGGAGCTGGAAAAACTTATACAATGCTTGGTACA
| | | | || || | |||| | ||||| ||| | ||| | | | | | | | | | || ||| | |||| ||| |||||| |||| || ||||||||||| |||||||||||||||| ||||| ||||||||||||||||| |||||||||||||| || |||||||| ||||||
---taattac-ccaaaattctgcattccttcaagtagttactggctcatttcttgattaggaagatgaaactttaacaaataaggtattgttttgaatttccagAACTGCAGAGCTAGTGGAAGCAGTATTGCAAGGGAGGAATGGGTCAGTGTTCTGTTATGGTGCCACAGGAGCTGGAAAAACATACACAATGCTGGGTACA
upper sequence: GLYMA18G22930.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S353_36V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgaca-gcactaatatgcggcatgcattcaaaatcttatagcttaggtgtactcatttatgtttgatggaaggtatacattgactttt-actttttcagAACCTCAGAACTTGTGGAAGCAGTTCTGCAAGGGAGGAATGGATCAGTTTTCTGTTATGGTGCCACCGGAGCTGGAAAAACTTATACAATGCTTGGTACA
| | | ||| | ||| | || | || || | ||| || || || || | | || | | |||| || |||| |||| || | |||| ||||||| ||| |||||||||||||| |||||||| || ||||| |||||||| || |||||||| || | |||||| | || ||
--tcatcgtggacttaaatggttcttggaatccaatcagtccagcctactggtcttctttgaaggttacagatactgatacgtttcttttttgaacactcagCACTGCCCAACTCGTGGAAGGAGTACTGCAAGGGAGGAACGGATCAGTATTTTGTTACGGTGCCACTGGTGCTGGAAAGACGCACACAATGTTAGGGACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggtgtactcatttatgtttgatggaaggtatacattgacttttactttttcagAACCTCAGAACTTGTGGAAGCAGTTCTGCAAGGGAGGAATGGATCAGTTTTCTGTTATGGTGCCACCGGAGCTGGAAAAACTTATACAATGCTTGGTACA
cattgac putative branch site (score: 3)
cttttactttttc CT-rich tract
ttttacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgacagcactaatatgcggcatgcattcaaaatcttatagcttaggtgtactcatttatgtttgatggaaggtatacattgacttttactttttcagAACCTCAGAACTTGTGGAAGCAGTTCTGCAAGGGAGGAATGGATCAGTTTTCTGTTATGGTGCCACCGGAGCTGGAAAAACTTATACAATGCTTGGTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - caaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggaagg