Sequence
atgc intronic sequence ATGC exonic sequencegtatctcaattcagtacaactttcataacataggctagttaagtgtacctagtcaatagtccacatccagcttattattgccttttgtttctaataagatcagGGGGTTGAGAATCGATTACCTTCTGAGCTATCTGGTGGAATGAAGAAAAGGGTTGCTTTAGCTCGTTCACTAATTTTTGATACAACAAAAGAGGTCATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65410.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 6
gtatctcaattcagtacaactttcataacataggctagttaagtgtacctagtcaatagtccacatccagcttattattgccttttgtttctaataagatcagGGGGTTGAGAATCGATTACCTTCTGAGCTATCTGGTGGAATGAAGAAAAGGGTTGCTTTAGCTCGTTCACTAATTTTTGATACAACAAAAGAGGTCATAG
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-tattcacactctgcttc-cttccattctagttgcatagccattatgttttccacacagactaactcctcacccccccccccccctctccccccttttttcaGGGAGTTGAGGATCGGTTGCCTTCTGAGTTATCAGGTGGGATGAAAAAGCGAGTTGCTTTAGCTCGATCTATTATTTGTGACACTACAAAGGAATCAATA-
upper sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 6
gtatctcaattcagtacaactttcataacataggctagttaagtgtacctagtcaatagtccacatccagcttattattgccttttgtttc-taataagatcagGGGGTTGAGAATCGATTACCTTCTGAGCTATCTGGTGGAATGAAGAAAAGGGTTGCTTTAGCTCGTTCACTAATTTTTGATACAACAAAAGAGGTCATAG
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---tctcaaaggatggaaaactaaagaaatcagctcaatcttctg-atggagaaaccttttttctttttggttatagggaaatttaacatagtgttttgtgcagGGCGTTGAGGAGCGGTTACCCTCTGAGTTGTCTGGTGGAATGAAGAAACGAGTTGCATTAGCTCGGTCTATTATTTTTGATACCACCAAGGATGCAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagtcaatagtccacatccagcttattattgccttttgtttctaataagatcagGGGGTTGAGAATCGATTACCTTCTGAGCTATCTGGTGGAATGAAGAAAAGGGTTGCTTTAGCTCGTTCACTAATTTTTGATACAACAAAAGAGGTCATAG
ttctaat putative branch site (score: 2)
ttttgtttctaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctcaattcagtacaactttcataacataggctagttaagtgtacctagtcaatagtccacatccagcttattattgccttttgtttctaataagatcagGGGGTTGAGAATCGATTACCTTCTGAGCTATCTGGTGGAATGAAGAAAAGGGTTGCTTTAGCTCGTTCACTAATTTTTGATACAACAAAAGAGGTCATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG