Sequence
atgc intronic sequence ATGC exonic sequencegtaatacaaaggattttattttgttatattgtcaatgcgatgagtctctttcgtattagtaacctcgataatccttttgcagTACACTTGGTCAAGGGCTTGAAACCAGCACATATCCTGGAGAGGTTATATTCTCTATAACACTTGCTATTGCTGGACTTCTACTATTTGCACTTCTCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G23980.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G23980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g55080.1 (Oryza sativa), 3'ss of exon 4
----------gtaatacaaaggattttattttgttatattgtca------atgcgatgagtctctttcgtattagtaacctcgataatcctttt--gcagTACACTTGGTCAAGGGCTTGAAACCAGCACATATCCTGGAGAGGTTATATTCTCTATAACACTTGCTATTGCTGGACTTCTACTATTTGCACTTCTCATT
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tttctgaagccaaagtcttatatgtctatatggctatgtcgatatctgatatttattgtccatcattcttatgactaacttccgtttccattttcatcagTACCCTTGGTCAAGGGCTTCAAACAAGCATATATCCTGGAGAGGTGTTATTCTCTATCGCAATATGTGTTATTGGGCTAATTCTTTTTGCTCTCCTCATC
upper sequence: AT2G23980.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G023037_T01 (Zea mays), 3'ss of exon 6
-----------gtaa-tacaaaggatt--ttatt-ttgttatattgtcaa-tgcgatgagtctctttcgtattag--taacctcgataatccttttgcagTACACTTGGTCAAGGGCTTGAAACCAGCACATATCCTGGAGAGGTTATATTCTCTATAACACTTGCTATTGCTGGACTTCTACTATTTGCACTTCTCATT
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ttctagctgttgtaggttcacaagattggctgtcatcattatatgttctacttcagagcgtgttatgcctgccatcttaatttccatttccattcgacagTACACTTGGTCAAGGGCTTTTGACAAGCACATACCCTGGAGAAGTCCTGTTCTCTATAGCAATATGTGTCCTTGGACTAATTCTTTTTGCTCTCCTCATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtcaatgcgatgagtctctttcgtattagtaacctcgataatccttttgcagTACACTTGGTCAAGGGCTTGAAACCAGCACATATCCTGGAGAGGTTATATTCTCTATAACACTTGCTATTGCTGGACTTCTACTATTTGCACTTCTCATT
tagtaac putative branch site (score: 1)
tccttttgc putative PPT
tattagtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatacaaaggattttattttgttatattgtcaatgcgatgagtctctttcgtattagtaacctcgataatccttttgcagTACACTTGGTCAAGGGCTTGAAACCAGCACATATCCTGGAGAGGTTATATTCTCTATAACACTTGCTATTGCTGGACTTCTACTATTTGCACTTCTCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA