Sequence
atgc intronic sequence ATGC exonic sequencegtattcaacaaatctcactattcataactatggggcaaaaatgttttctgtaacttagttaagtaagaatccaatctctagatagaatatggtcatcagtcatgaccataaacatagagaccagttattgatgttgttataattggcagGTGATTAATTATAAAACTCAGCAGAACAGGTTGTTTCCTCTGCTGGCATCTGCATATGCATTTCGGTTTGTAGGGGAATGGCTGAAGTGGCTCTACACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35690.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 7
gtattcaacaaatctcactattcataactatggggcaaaaatgttttctgtaacttagttaagtaagaatccaatctctagatagaatatggtcatcagtcatgaccataaacatagagaccagttattgatgttgttataattggcagGTGATTAATTATAAAACTCAGCAGAACAGGTTGTTTCCTCTGCTGGCATCTGCATATGCATTTCGGTTTGTAGGGGAATGGCTGAAGTGGCTCTACACTG
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-----------------------------------ttaatatttgtactttg-ttcatctaa--aagaattaaattgataaac-gagtttaactttttgctacca--------atgacaagtggctaatggt-ctataatggtta-cagGTCCTCAATTACAAGACTCAGCAAAGCAGACTCTTTCCTTTGCTGGCTTCAGCTTATGCATTTAGGTTTGTGGGTGAGTGGCTGAAGTGGCTGTACACGG
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 7
gtattcaacaaatctcactattcataactatggggcaaaaatgttttctgtaacttagttaagtaagaatccaatctctagatagaatatggtcatcagtcatgaccataaacatagagaccagttattgatgttgttataattggcagGTGATTAATTATAAAACTCAGCAGAACAGGTTGTTTCCTCTGCTGGCATCTGCATATGCATTTCGGTTTGTAGGGGAATGGCTGAAGTGGCTCTACACTG
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------------------------------------gaatcaactgcccg---cccagt---gttaccacctgtgcttaacatggaaaatg--catctgtc--ggttaccaacaaaaggt---gtctaacatattcaagctggttacagGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcagtcatgaccataaacatagagaccagttattgatgttgttataattggcagGTGATTAATTATAAAACTCAGCAGAACAGGTTGTTTCCTCTGCTGGCATCTGCATATGCATTTCGGTTTGTAGGGGAATGGCTGAAGTGGCTCTACACTG
tattgat putative branch site (score: 3)
atgttgttataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcaacaaatctcactattcataactatggggcaaaaatgttttctgtaacttagttaagtaagaatccaatctctagatagaatatggtcatcagtcatgaccataaacatagagaccagttattgatgttgttataattggcagGTGATTAATTATAAAACTCAGCAGAACAGGTTGTTTCCTCTGCTGGCATCTGCATATGCATTTCGGTTTGTAGGGGAATGGCTGAAGTGGCTCTACACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG