Sequence
atgc intronic sequence ATGC exonic sequencegtaattgctttggaacctaatagatctttgaatactttgctctctcaccgttctgccctgaactattttgtatttttgtagGTACAAGTTCACTCTGTTCAATGAGCTTTACTTTTTGGTTGCCGGTGGTACAGTTTGGATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24180.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24180.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os10g33420.1 (Oryza sativa), 3'ss of exon 14
-----------------------------------------gtaattgctttggaacctaatagatctttgaatactttgctctctcaccg---------ttctgccctgaactattttgtattt--------ttgtagGTACAAGTTCACTCTGTTCAATGAGCTTTACTTTTTGGTTGCCGGTGGTACAGTTTGGATAG
|| || | | || | | | | || | | |||| || | ||| || | ||||| | ||| ||| |||||||||||||| || || ||||||||||||||| |||| || || ||||| ||||||| ||
gtacaaccttagttctatatttctttctgaactgatgtgttctacttcttcagtaaagaactttggcagtaaacatctaaatctcccaaagaaaaacaaaatcttaactagaatatttggggtttcatggtgcttgcagGTACAAGTTCACACTTTTTAATGAGCTTTACTTTCTGGTAGCTGGGGGTACTGTTTGGACAG
upper sequence: AT3G24180.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM5G895188_T02 (Zea mays), 3'ss of exon 4
------------------------------------------gtaattgcttt---ggaacctaatagatctttgaatactttgctctctcaccg---ttctgccctgaactattt---tgt----atttttgtagGTACAAGTTCACTCTGTTCAATGAGCTTTACTTTTTGGTTGCCGGTGGTACAGTTTGGATAG
|| |||| || | || || || | | || || | | || | | | | ||| ||| || ||| ||||| ||||||||||| || ||||||||||||||| |||| || || || || ||||||| ||
gtatatactatactctacctctattgctcctatattaagtttgttgttgccttccagaaatttactactccacatcttcctctgtagagaaaatgaaatttaactgtagaatgtttgggtgttgaaatgcttgcagGTATAAGTTCACTCTTTTTAATGAGCTTTACTTTCTGGTAGCTGGGGGGACTGTTTGGACAG
upper sequence: AT3G24180.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv05s0051g00910.t01 (Vitis vinifera), 3'ss of exon 12
---------gtaattgctttggaac-ctaatagatctttgaatactttgctctctc---accgttctgccc--tgaactattttg----tatttttgtagGTACAAGTTCACTCTGTTCAATGAGCTTTACTTTTTGGTTGCCGGTGGTACAGTTTGGATAG
|| || || || | | ||| | | || || | | || | | || || || || ||| ||| | || |||||||||||||| | || ||||| || |||||||||||||| ||||| ||||||||||| |
cctctgcttgtgatgaagctgaaatattcacagaacataatattctagaccttttccttatcattgtggtagatgtgtgatgttgatgttatgtgtgcagGTACAAGTTCACGTTATTTAATGAACTCTACTTTTTGGTTGCTGGTGGGACAGTTTGGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgaatactttgctctctcaccgttctgccctgaactattttgtatttttgtagGTACAAGTTCACTCTGTTCAATGAGCTTTACTTTTTGGTTGCCGGTGGTACAGTTTGGATAG
ctctcac putative branch site (score: 3)
tattttt putative PPT
aactattttgtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgctttggaacctaatagatctttgaatactttgctctctcaccgttctgccctgaactattttgtatttttgtagGTACAAGTTCACTCTGTTCAATGAGCTTTACTTTTTGGTTGCCGGTGGTACAGTTTGGATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT