Sequence
atgc intronic sequence ATGC exonic sequencegtatcacaaaatatagtaaataccttaaagctagctatacatacttatagagatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54450.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
gt-atcacaaaatatagtaaataccttaaagctagctatacatacttatagagatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
|| ||||||| | | | || |||||| | | ||| || || | || | || | || | |||| || | |||||| || | || ||||||||||| || || |||||||| |||||||| | || ||||||||||||| ||||||||||| |||||||
gtgatcacaacttct------tgccataaagcag--tgaattcactgttaatcatctaaataacaagttggatcatctttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
gt-atcacaaaatatagtaaataccttaaagctagctatacatacttatagagatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
|| || | || || |||| | ||| | | | || | | | ||| ||| |||| || |||| ||||| || | |||||| || || |||||||| || ||||| ||||||||||||||||| | || ||||||||||||| || |||||||| |||||||
gtgattataatccttaataaa--ctttagatttgctgccaagtattaagttaaata---attggctaatgtttaattg--------tagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 11
-----------gtatcacaaaatatagtaaataccttaaagctagctatacatactta--tagagatattca-tttctcaatgattgat-tgctgatac-------atagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
| | | ||||| || | || | | || ||| ||| || ||| || | || | | || || | |||| | ||| || |||||| || | || || |||| ||||||||||||||| ||||||||| |||||||||||||||| ||||||||||||||||| |||||||| ||||||||||
gtgcatgaaatatttgataaaatttattgcattctt--gagttag-tatgtatgcttggctactgttagtgacttccttggtaattggtatgcatatcttgtgtgaatagGAACGTGAGAACCCAACATTGACAGAGTGGGATCGATTTGCTCATCGAGAATATATTAGGCTTTCAATGGAAGAAGATGTAGAAGATGCCTCTAATGGAA
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 11
--------gtatcacaaaatatagtaa--ataccttaaagctagctatacatacttatag-----agatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
||| | || | || | | | | || || ||| | ||| | | | || | | | || | | | |||| || | ||||| |||| ||||||||||||||| |||||||||||||||||||||||||| || |||||||||||||| || ||||| ||||| || |
gtgcatgaatatttgataaaagtgttattgtgctgttgagtcag-tatgattgactattgttggtaagttttgactgccttggtatatgtcttgtgtgaacagGAACGTGAGAATCCTACATTGACAGAGTGGGATCGCTTTGCTCATAGAGAATATATTAGGCTTTCTATGGAAGAAGATGTAGAGGATGCCTCTAACGGTA
upper sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 11
-----------gtatcacaaaatatagtaaataccttaaagctagctatacatactta--tagagatattca-tttctcaatgattgat-tgctgatac-------atagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
| | | ||||| || | || | || ||| ||| || ||| || | || | | || || | |||| | ||| | |||||| || | || || |||| ||||||||||||||| ||||||||| |||||||||||||||| |||||||||||||| | |||||||| ||||| ||||
gtgcatgaaatatttgataaaatttattgcattgtt--gagttag-tatttatgcttggctactgttagtgacttccttggtaattggtatgcatgtcttgtgggaatagGAACGTGAGAACCCAACATTGACAGAGTGGGATCGATTTGCTCATCGAGAATATATTAGGCTTTCAATGGAAGAAGACATAGAAGATGCCTCTAACGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctatacatacttatagagatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
tgctgat putative branch site (score: 3)
atattcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcacaaaatatagtaaataccttaaagctagctatacatacttatagagatattcatttctcaatgattgattgctgatacatagGAGCGCGCAAATCCGACATGGACAGAGTGGGATCGTTTTGCTCATAGAGAATATATTAGGCTATCAATGGAAGAAGATGTCGAAGATGCTTCTAATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG