Sequence
atgc intronic sequence ATGC exonic sequencegtcagtcccttactgtcctttttttcatctgaaaatatgtgccgttgttttgatgttgatagtcttctttttgttttgttttataatcctgttttagCAGCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G13880.1 (Glycine max), 3'ss of exon 2
gtcagtcccttactgtcctttttttcatctgaaaatatgtgccgttgttttgatgttgatagtcttctttttgttttgttttataatcctgt--tttagCAGCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTT---
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--gtataacatactttcctctgtgtaatctttta-tgttcaacaat-ttttgatgttttgtttatgcagtttcatttggccaatctttttttaatttcacagCTAAAGTTTCCATCAGCACTAGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGGAAGAGAATAGCATTGTTTCTGGATTATGATGGGACTCTTTCAC
upper sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G47630.1 (Glycine max), 3'ss of exon 2
-----gtcagtcccttactgtcctttttttcatctgaaaatatgtgccgttgttttgatgttgatagtctt---ctttttgttttgttttataatcctgttttagCAGCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTT---
|||| |||| | | | ||| | | ||| | || ||| | | || | || ||| |||| | | | ||| ||||| |||| ||||||||| ||| | |||||||| |||| | | | ||||||||| || ||||||||||||||||| |||||||| || || ||||
gtataacatactttcctctgtaattttgtatgttcaataattttggatgttttgtttatgcagttgcattttaccaccttaattttttttttttttttaatttcacagCTAAAGTTTCCATCAGCACTTGCATCTTTTGATCAAATTACCAACTGTGCAAAAGGAAAGAGAATAGCATTGTTTCTGGATTATGATGGAACTCTTTCAC
upper sequence: AT5G51460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 1
----gtcagtcccttactgtcctttttttcatctgaaaat-atgtgccgttgttttgatgttgatagtcttctttttgttttgttttataatcctgt--tttagCAGCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTT---
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gtaaattttgccccctttgtgttgtgtaactttggaggctcatctttgatggaaccctagatggctgactgacttagttcctgccctcttttcttgtgattttgcagCTTAAGTATCCATCAGCACTTAAATCTTTTGAGCAAATCACGAACTATGCCAAGGGAAAAAGAATAGCATTGTTTCTGGACTATGATGGGACTCTCTCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgttgttttgatgttgatagtcttctttttgttttgttttataatcctgttttagCAGCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTT
tgttgat putative branch site (score: 4)
tcctgtttt putative PPT
ttctttttgttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtcccttactgtcctttttttcatctgaaaatatgtgccgttgttttgatgttgatagtcttctttttgttttgttttataatcctgttttagCAGCTCAAGTATCCATCAGCTCTTACCTCTTTTGAGAAAATCATGAGTTTTGCAAAAGGCAAAAGAATAGCATTGTTTCTTGATTATGACGGGACACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA