Sequence
atgc intronic sequence ATGC exonic sequence...agtcaatcacctgtggatgagataggttcaaaacccaaatttttacttgtatcactttgttatagcaggctgtaactttttttcgtccaccattctctagGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAGGAAGTAATTTTGACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G13370.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 18
agtcaatcacctgtggatgagataggttcaaaacccaaatttttacttgtatcactttgtta---tagcaggctgtaactttttttcgtc-caccattctctagGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAGGAAGT---AATTTTGACAAG
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---ggaacgcgcaaagaaaaagatggttgtcaaagtgcattgtt-catgtattctttagtaggattattgaactgttctttttacctattgtttcctatttcagGTTCTTGATCACTTGGTTATTCAGAAGCTAAATGCTGAGGGCAGGCTTGAGAAGAAAGAATCCAAAAAGGGTGGCTCCATATTTGACAAG
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 20
agtcaatcacctgtggatgagataggttcaaa----acccaaatttttacttgtatcactttgttatagcaggctgtaactttttttcgtcca---ccattctctagGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAGGA---AGTAATTTTGACAAG
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-------tatttttatatatttttcccctaaaagacatgcaattgcttattgacatgccttgaggtcaataattttatgtcatttttcatgtgaatgtgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 20
--------------------------------------------------------------------------agtcaatcacctgtggatgagataggttcaaaa----cccaaatttttacttgtatcactttgttatagcaggctgtaactttttttcgtccac---cattctctagGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAG---GAAGTAATTTTGACAAG
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gtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttattgccatgccttgaggtcaacaattttatatcatttttcatgtgaacatgttccatagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 20
---------------------------------------------------------------agtcaatc-acctgtggatgagataggttcaaaacccaaatttttacttgtatcactttgttatagcaggctgta-actttttttcgt-ccaccattctct------agGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAGGAAGTAATTTTGACAAG
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gtaaaccaaacatttctttgtctatgcttaaatccttttcttttcatactgtttatatttaaaagcatgtctgtttgcacacatggtggattatatggtct--ctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGGGGAGTTACTTTGACAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtatcactttgttatagcaggctgtaactttttttcgtccaccattctctagGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAGGAAGTAATTTTGACAAG
ctgtaac putative branch site (score: 3)
ctttttttcgtccacc CT-rich tract
taacttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtcaatcacctgtggatgagataggttcaaaacccaaatttttacttgtatcactttgttatagcaggctgtaactttttttcgtccaccattctctagGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAGGAAGTAATTTTGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -caatcac
- - - - - - - - - - - - - - caaaacc