Sequence
atgc intronic sequence ATGC exonic sequencegtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61960.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
---------gtacagtct-catattgct-----gctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
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ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatcccttt-tttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
-------------------------------------------------------------------------gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
|| | | || ||| || | | | | || ||| || | | || ||| | |||||||| ||||||||||| ||||| || || |||||||||||| | ||| | |||||| | |||||||||||||||||||| ||||| |||||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------gtacagtctcatattgctgctttttcttatggcttttgtcct---tttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
|| | | | || || || | || ||| | | | | | || | || ||| |||||||| ||||||||||| ||||| || || |||||||||||| | ||| | ||||| | ||||||||||||||||| || ||||| |||||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------gtacagtctcatattgctgctttttcttatggcttttgtccttttggga--gagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
| | || || | | |||| || || | | | ||| ||| | || | || || | | |||||||||||| ||||| ||||||||||| |||||||| || |||||||||||| | ||| | |||||||| || ||||| ||||| ||||||||||| |||||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacatt--cacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
| | | | | | | |||| | | | | ||| || | | || ||||| | || |||||||| || ||||| ||||| || ||||||||||||||| |||| |||| || || |||||||| || | || || || || || ||||
---------------gttctctgtgaaaaagagagaggagattttcctacgacttggttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
ggctaaa putative branch site (score: 3)
tcttaaaaaaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC