Sequence
atgc intronic sequence ATGC exonic sequencegtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G02890.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
--------gtattgatcacttaaaacggttacctg---actctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
| || | || | | | || | | || ||| | | | || | || | | | |||||||||| || |||||||| || || |||||||||||||| ||||||||||| |||||||||||||| || || ||||||||
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgtttttt-ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
||||| || | || || | |||| || | | | | | || | | | | | | ||||||||||||| || |||||||| || || ||||||||||| |||||||||| ||||| || || || || ||| ||||||||
gtatt-atttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagatt-agacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
||| | || || | | ||||||| | || || || | ||||||||||||| || |||||||| || || ||||||||||| |||||||||| ||||| || || || || ||| ||||||||
-----------------gtattatttcacctaatgg-gcaactgatgagattcactactgtctcaagGCT--AACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
||||| | | ||| | |||| || || | | | | || | | | || | | ||||||||||||| || |||||||| || || ||||||||||| |||||||||| ||||| || || || || ||| | ||||||
gtattatttgacctag-cgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 2
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
||||| || | || || | |||| || | | | | | || | | | | | | ||||||||||||| || |||||||| || || | ||||||||| |||||||||| ||||| || || || || ||| ||||||||
gtatt-atttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGTTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 4
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCAT-TTTTGTTGATGAG---------------
||||| || | || || | |||| || | | | | | || | | | | | | ||||||||||||| || |||||||| || || ||| ||||||| |||||||||| ||||| || || || || |||| ||||||||
gtatt-atttcacctaatgggcaactgatgagattcactactgtctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTATTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTTATTGATGAGGTATGCAAGCACACA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
gtattgatcacttaaaacggttacctgactctatagtgt-tttctttgagattagacttgacttgaga------------tttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
||||| || ||| ||||| | | | | |||| |||| ||| |||| || | ||| || ||||||||||||| ||||||||||| || |||||||| || ||| |||| || || || |||||||| || ||||||||||| |||
gtattaatgttgtaa----gttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
ttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgatcacttaaaacggttacctgactctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG