Sequence
atgc intronic sequence ATGC exonic sequencegtaacatccttaaacccgttttgttgtaacgcatccgtaaacgttagtcatgtgcagttatcgtaggtgcgtttgatagtttgtttcacttgttcaccttctcatgtcttgtcagGTGGTTATGCAGCTGGATACTACAGTTACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10540.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 13
gtaacatccttaaacccgttttgttgtaacgcatccgtaaacgttagtcatgtgcagttatcgtaggtgcgtttgatagtttgtttcacttgttcaccttctcatgtcttgtcagGTGGTTATGCAGCTGGATACTACAGTTACAAG
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---------------------gtttgcaatgcttt----aaccta---catgtacattcattc---atttatttgactgcagatctcactattttttttattgacaatctg-cagGAGGCTATGCAGCTGGATACTACAGTTACAAG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 13
gtaacatccttaaacccgttttgttgtaacgcatccgtaaacgttagtcatgtgcagttatcgtaggtgcgtt--tgatagtttgtttcacttgttcaccttctcatgtcttgtcagGTGGTTATGCAGCTGGATACTACAGTTACAAG
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------------------------------------gtttgcgccactcttttctctctctctctctcaagttggtgacaggatgacctctcatttcattat---gggcaattgcagGTGGCTATGCTGCTGGATACTACAGTTACAAG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 13
gtaacatccttaaacccgttttgttgtaacgcatccgtaaacgttagtcatgtgcagttatcgtaggtgcgtttgatagtttgtttcacttgttcaccttctcatgtcttgtcagGTGGTTATGCAGCTGGATACTACAGTTACAAG
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----------------------gtt-tgatgtgcctct---tgtttctctt-tgtaattatgctagtgtctcaacaaaactaaatttatttattctgggttttgc-ttttgttagGTGGATATGCAGCTGGATACTATAGTTACAAG
upper sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 16
gtaacatccttaaacccgttttgttgtaacgcatccgtaaacgttagtcatgtgcagttatcgtaggtgcgtttgatagtttgtttcacttgttcaccttctcatgtcttgtcagGTGGTTATGCAGCTGGATACTACAGTTACAAG
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----------------------gtt-tgccttttctgttaatttt-gctaaatacagcagtttt-----tccttgtgaatttatct--cttattg--cttcttgtgaat-atcagGTGGATACGCAGCTGGATACTATAGTTACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgtaggtgcgtttgatagtttgtttcacttgttcaccttctcatgtcttgtcagGTGGTTATGCAGCTGGATACTACAGTTACAAG
gtttgat putative branch site (score: 5)
ccttctcatgtctt putative PPT
tttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatccttaaacccgttttgttgtaacgcatccgtaaacgttagtcatgtgcagttatcgtaggtgcgtttgatagtttgtttcacttgttcaccttctcatgtcttgtcagGTGGTTATGCAGCTGGATACTACAGTTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA