Sequence
atgc intronic sequence ATGC exonic sequencegcaagttttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttctggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G36160.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 17
gcaagt--tttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttctggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
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gtaacttattattttttttatactttattattaattagttggataaatg-gttttg---------atttcatgatggttctgattgttgaact-------gcaatgactccagTTGGATGGAAACAGCCATGTGATTTATGCAGAAGAAGAAGCTGGCGGTACACGGCTTCAGATTAATGGAAAGACATGCTTGTTGCAG
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 17
gcaagttttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttc--tggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
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-----------------------------gtaactagttcttttttatgctttattattaattagttggataaatggtttcgatttctgattgttaaactgcaatggctccagTTGGATGGAAACAGCCATGTAATTTATGCAGAAGAAGAAGCTGGTGGTACACGGCTTCAGATTGATGGAAAGACATGTTTATTGCAG
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
gcaagttttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttctggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
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---acacagtggtattttatcgata--acatcactattttataactg-gtcttttgttctata---tctggtacttgagttattaactagcagtttccact--tgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 16
gcaagttttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttctgga-gaatctcacttccttttcttgttttcactg-tcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
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------------acacagtggtattttatc-gataacatcactattttataactggtctgttgttctatatctgattcttgagttattaactagcagttgccaattgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
upper sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 17
--gcaagttttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttctggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
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tatctaggaggttgactttggtgggaattatgatccaaag---tagtctcttctgtttggtcaacacttccgaa---------ttgtttttgatagtttcagt-ttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaaaaacttctggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
atctcac putative branch site (score: 3)
tctcacttccttttct CT-rich tract
ttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagttttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttctggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC