Sequence
atgc intronic sequence ATGC exonic sequence...cttagatttgttagaaatgatattgagaggtctacctggttctagtactccattgagttgtcctgcaaaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52360.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 9
---cttagatttgttagaaatgatattgagaggtctacctggttctagtactccattgagttgtcctgcaaaacc--ttaccttgtccacattctcattt-cacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
|| || ||||| | || | | | || || | || || || || | || | | | | | | | || ||||||||||||||||||||||||||| || || ||| | ||| |||| || ||| ||||||| ||||||||||||| | ||||||||||||||| | ||
caatttgctcttcacagaaacccttttc-----ttttcatgttttcattaacttcttccttt-tcaagttaatttagtgatacgggaaaaaacttgacttgtgcagGGTTGTGATCGGATATGATGAAGGGACAATAATGATAAAAATTGGCCGTGAAGTTCCTGTTGCTAGCATGGACAGCAGTGGAAAAATCATATGGTCAAAA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 9
----cttagatttgttagaaatgatattgagaggtctacctggttctagtactccattgagttgtcctgcaaaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
|| | || || | || ||| | | | | | | | | | | | ||| | || | | | | | || | || ||||||||||| |||||||||||||| || || ||| | ||| |||| || ||| ||||||| ||||||||||| | | |||||||| |||||||| |||
aagaatttctctcattgaaacatgttgtgtgagattttcattgacttgttctttcctgcataagtcaagttaa---tgatatggaatattttatt-ttgtgtagGGTTGTGATTGGATATGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 9
cttagatttgttagaaatgatat-----tgagaggtctacctggttctagtactccattgagttgtcctgcaaaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
|||| ||||| | ||| | ||||| | || ||| | | | | | | | ||| || || | | || | | | || ||||||||||| ||||| |||||||| || || ||| | ||| |||| || ||| ||||||| ||||||||||| | | |||||||| |||||||| |||
taaagatatgttatcactgaaacatgtgtgagatttttaattggct-tgttctttcctgcataagtcaagctaa----tggcatggaaaaacttattttgtgtagGGTTGTGATTGGATACGATGAAGGGACAATAATGATAAAAATTGGTCGTGAAGTTCCTGTTGCTAGCATGGATAGCAGTGGAAAAATTATATGGGCAAAG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 9
--------------------------------------------------cttagatttgttagaaatgata--ttgagaggtctacctggttctag-tactccattgagttgtcctgca---aaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
||| | | | || | | | || | | || || | | || | || || | || ||| || || | | ||||||||||||| || |||||||||||||| || ||||| |||||||| |||||| ||||||| |||||||||||||| | ||| ||||| || ||| |||||
gtaagttttttgtggatagaatttttgcaattaatttcttaatataattttttaagcccttgaatagtgctgagtgggaagctgtgccaaattgtgcctgaattatgaaattttcttatccttaactcttttctcgtatcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTTCCTGTGGCTAGCATGGACAACAGCGGGAAAATTATTTGGTCTAAG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
-------------------------------------cttagatttgttagaaatgatattgagagg-tctacctggttctag-tactccattgagttgtcctgca---aaaccttaccttgt---ccacattctca-------tttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
||||| | | ||| | || || | | | || | | || | || || | || ||| || | | | ||| || | ||||||||||||| || |||||||||||||| || ||||| |||||||| |||||| | ||||| |||||||||||||| | || ||||| || ||| |||||
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 9
------cttagatttgttagaaatgatattgagaggtctacctggttctagtactccattgagttgtcctgcaaaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
| |||| | | | |||||| || || ||| ||| || | | || | |||| | | | ||| || |||||||||||| || ||||||||||| || || ||||| |||||||| |||||| ||||| || |||||||| || | || ||||| || |||||||||
tgccgaatattatttactttttcttctcttgagaaatcag--tgtctct----ctcttttccctccttcttcgtgacctaaattaccaaaacctctttctttgcagGGTTGTGATAGGCTATGATGAAGGTACTATTATGGTCAAACTTGGCCGAGAAGAACCTGTAGCCAGCATGGATAACAGTGGGAAAATAATTTGGGCTAAG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 9
cttagatttgttagaaatgatattgagaggtc---tacctggttctagtactccattgagttgtcctgcaaaac---cttaccttgtccacattctcatttca--cagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
||| | | | | | | || || | | ||| | | | | | | | || ||| || | | | | | || ||||||||| ||||| ||||||||||||| || ||||| |||||||| ||||| | ||||| || || |||||||| | |||||||| ||||||||||||
--------tgtcacacttcacttctcttgttcctgtagccagcactaaatatttagtatatggcttaggagaaatggcttggaatgactattattgctctccatccagGGTTGTAATCGGCTATGATGAAGGAAGTATTATGGTAAAACTTGGTAGAGAAGTGCCTGTGGCAAGTATGGACAACAGTGGAAAAATAATATGGGCTAAG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 9
----cttagatttgttagaaatgatattgagaggtctacctggttctagtactccattgagttgtcctgcaaaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
||| ||| || ||| || | | || || | |||| || || | | | | | | | | | ||| | || |||||||||||||||| | ||||||||||||||| ||||| ||| |||| ||||| || || ||||| ||||| |||| ||||| ||||||||||||||
aaaatataggtttattttgaataattgttatcacactctctcaatatagttgctgtatgctttattc----acatgtggcttctttttctttcctactttacagGGTTGTGATCGGTTTTGATGAAGGAACCATTATGGTGAAAATTGGTCGAGATGAACCAGTAGCTAGTATGGATAATAGTGGAAAGATCATATGGGCTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactccattgagttgtcctgcaaaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
accttac putative branch site (score: 3)
ttctcatttc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttagatttgttagaaatgatattgagaggtctacctggttctagtactccattgagttgtcctgcaaaaccttaccttgtccacattctcatttcacagGGTTGTGATCGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAATACCGGAAAAATCATATGGGCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - gatttgt
- - - - - - agaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacatt