Sequence
atgc intronic sequence ATGC exonic sequencegttcccccatttattctcaagcatttttaccttttatatttcatcagcatacacaaacactgaacctttggggttgacgtgtgtaattccagAAAAACTACATCAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAAGAGGTTCTCATGGATTTCTTTAGGGAGTATATAAGTGCATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71820.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 16
---------gttcccccatttattctcaagcatttttaccttttatatttcatcag-catacacaaacactgaacctttggggttgacgtgtgtaattccagAAAAACTACATCAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAAGAGGTTCTCATGGATTTCTTTAGGGAGTATATAAGTGCATCT
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ttatgcctgacagcctgaggaggtctttcaaaaaccaatctcacaactgctgtctgacatgtcctttcattacttaatatgtgttcccttgcgt--ctgtagAAAAACTACATAAAAGAAGAAACGATAGAGAGGATGAGGTTAGATGAAGAGGTGCTTATGGATTTCTTCAGGGAACACATCAACGTGACA
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G161553_T01 (Zea mays), 3'ss of exon 3
-----------gttcccccatttattctcaagcatttttaccttttatatttcatcagcatacacaaacactgaacctttggggttgacgtgtgtaattccagAAAAACTACATCAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAAGAGGTTCTCATGGATTTCTTTAGGGAGTATATAAGTGCATCT
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atgtaagattatgtctgagaagaacattcaaaaacta--atctcacactgctgtttgacatgtccttccaatagttaatatgtatttcctt-tgcgtctgtagAAAAACTACATAAAAGAGGAAACAATAGAGAGGATGAGGTTAGATGAAGAGAAGCTTATGGATTTCTTTAGGGAACACGTCAACGTGACA
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA03G03120.2 (Glycine max), 3'ss of exon 22
-----------------------gtt--cccccatttattctcaagcatttttaccttttatatttcatcagcatacacaaacactgaacctttggggttgacgtgtgt---aattccagAAAAACTACATCAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAAGAGGTTCTCATGGATTTCTTTAGGGAGTATATAAGTGCATCT
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gttctgatgtcaataaaacagttgttggcttttatttatgtactaaaattgt-gcatattttcttctaacagctt-tgtatttatttgacttaattgttccactgatattttaattgcagAAAAATTACATTAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAGGAGGTTATCATGGACTTTTTTAGGGAACATATCAGTGTTTCT
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 21
----------------------gttcccccatttattctcaagcatttttaccttttatatttcatcagcatacacaaacactgaacctttggggtt----gacgtgtgtaattccagAAAAACTACATCAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAAGAGGTTCTCATGGATTTCTTTAGGGAGTATATAAGTGCATCT
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gtttttgttgaaaagaatttatagtttcccatttgttgg-atatatttttgtatgt-atcctcctgtaatatcttttgtttccttgcatgaatggcttaatgatgcttgtgattgcagAGAAACTATATAAAGGAAGAAACCATTGAACGGATGAGGCTAGATGAAGAGGTTATCTTGGATTTCTTTAGGGAGTACATAAGTGTCTCC
upper sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 21
----------------------gttcccccatttattctcaagcatttttaccttttatatttcatcagcatacacaaacactgaacctttggggtt----gacgtgtgtaattccagAAAAACTACATCAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAAGAGGTTCTCATGGATTTCTTTAGGGAGTATATAAGTGCATCT
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gtttttgttgaaaagaatttatagtttcccatttgttgg-atatattttgatatgt-attctcctgtaatatattttgtttccttgcgtgaatggtttaatgatgcttgtgattgtagAGAAACTATATAAAGGAAGAAACCATTGAACGGATGAGGTTAGACGAAGAGGTTATCTTGGATTTCTTTAGGGAGTACATAAGTGTCTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcatcagcatacacaaacactgaacctttggggttgacgtgtgtaattccagAAAAACTACATCAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAAGAGGTTCTCATGGATTTCTTTAGGGAGTATATAAGTGCATCT
ggttgac putative branch site (score: 4)
tgtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcccccatttattctcaagcatttttaccttttatatttcatcagcatacacaaacactgaacctttggggttgacgtgtgtaattccagAAAAACTACATCAAGGAAGAAACTATTGAACGGATGAGGCTAGATGAAGAGGTTCTCATGGATTTCTTTAGGGAGTATATAAGTGCATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA