Sequence
atgc intronic sequence ATGC exonic sequencegtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G38360.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g51100.2 (Oryza sativa), 3'ss of exon 7
gtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
|||| ||| || | || |||| || | || | | | | | | || | | || | | |||||| |||| || || ||||| |||||||||||||||||||| || || ||||||||||||||||||| ||| | || ||||| || || || ||
-------------------------gcagt--taaaatgatgttt--ccttttcgtttttttattgttactcagtaaaaagtaggagcactagcttgctgatgctgaactaataacccctatctaccagGTACTCTTACACTGCTGTGGTTCTCAATTTTAGTCAGTCATGGGCCTTGTATTGTCTGGTTCAGTTCTATGCTGCCATAAAGGATGAACTAGCCCATATA
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G088737_T01 (Zea mays), 3'ss of exon 6
gtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
| || ||| || || || ||| | | || | | | || | ||| | | | || | | || || | | || || |||| ||| | | |||||| |||| ||| || ||||| ||||| |||||||||||||| ||||||||||| ||||||||||||| || | || |||||| | || || ||
----------attatgttgc--agcgcactgtgaacttgctcatgcatttgatgacataggaatta-----aacaatcgttgtcttc--ccattactgaagtat-ttac--ttgcctacc-------agGTACTCTTACACGGCTGTGGTTCTCAATTTCAGTCAGTCATGGGCCTTATACTGTCTCGTTCAGTTCTATGCTGTGATAAAGGATGAGTTAGCTCATATA
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G373717_T01 (Zea mays), 3'ss of exon 5
-------gtacgttgagacaattttgacaagaaca-gtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
| | | ||||| | ||| |||||| | | | | || | | | | | | ||| ||| || | || | || | || ||| || | | |||||| |||| ||| || ||||| ||||| |||||||||||||| ||||||||||| || |||||||| | | || |||||| | || || ||
gtaagaggcatat-actttttttttgttttgcacatgtgctagct--ctggtcaacttgctcatgc---atttgatggcataggaaatgaacaatcattgccttgccattactgaactatttacttatctacc--agGTACTCTTACACGGCCGTGGTTCTCAATTTCAGTCAGTCATGGGCCTTATACTGTCTCGTCCAGTTCTACACCGTGATAAAGGATGAGTTAGCTCATATA
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G00250.1 (Glycine max), 3'ss of exon 4
gtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
| | | | ||| ||| || || | | | | | | | ||| | | | ||| ||||| || || | | ||| |||||||||| |||||| ||||||| ||||||||||| |||||||||||||| || ||||| || ||||| || ||| | || || || || || || || ||
-------ggtatcttcattttaaggtttgtgttattatgctgttctag--tgataggtaaaagtt--ctcaagttatatctgactgca--tgagctatctgg----taca------------tttgtagGTATCCTTATATGGCAGTGGTTCTAAATTTCAGTCAGTCATGGGCTTTGTACTGCCTTGTTCAATTTTATACAGTTACAAAGGACGAACTGGCTCATATA
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G00300.1 (Glycine max), 3'ss of exon 4
gtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
| | | | |||| ||| || || | | | | | | | ||| | || | ||| ||||| | || || | | ||| |||||||||| |||||| ||||||| ||||| ||||| |||||||||||||| || ||||| || ||||| || ||| | || || || || || || || ||
-------ggtatcttcattttaagatttgtgttattatgctgttctag--tgacaggtaaaagtt--ttgaagttatatctgactgc--ttgagctatctgg----taca------------tttgtagGTATCCTTATATGGCAGTGGTTCTGAATTTCAGTCAGTCATGGGCTTTGTACTGCCTAGTTCAATTTTATACAGTTACAAAGGAAGAACTGGCTCATATA
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0038g03670.t01 (Vitis vinifera), 3'ss of exon 6
gtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgt----tttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
|| |||| | || |||| | | | || | | ||| |||| || | |||||| |||| || |||||||||||| ||||| | ||||| ||||||||||| ||||| |||||||| | ||||| | |||||||| ||| || || || ||||| | | |||||
------------------------------------gta-agatag---tttggaaataattgttggaaa-attttttgctaact-tgatttgtttaaatgtctcttacagttgtagacttctgtttttgtagGTATCCTTACATAGCAGTGGTTCTAAATTTCAGTCAATCATGGGCTCTGTACTGCTTAGTTCAGTTTTATACTGTTACAAAGGATGAATTGGAGCACATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
atcttac putative branch site (score: 3)
tcttaccattgttttc CT-rich tract
attgttttctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT