Sequence
atgc intronic sequence ATGC exonic sequence...aatagacgtattatctggctgaataatatataattccgtttcgttattcagacatccaattatcttgatagattggattattgtctttcttatggttcagCATGGGGGCTGGATGTTCTCAACTCTTGTCTGACATGCAGGCTTTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55060.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G10700.1 (Glycine max), 3'ss of exon 2
aatagacgtattatctggctgaataatatataattccgtttcgttattcagac-atccaattatcttgatagattggattattgtctttcttatggttcagCATGGGGGCTGGATGTTCTCAACTCTTGTCTGACATGCAGGCTTTCAAG
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atttcactgcatatctgcatttatgatctaataggttctagacttatagttactatagggtaggcatttcataatagttttctttactttgtatg-ctcagTGTTGGTGCTGGATGCTCTCAACTCCTCTCTGATATGCAGGCTTTCAAG
upper sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G43140.1 (Glycine max), 3'ss of exon 7
aatagacgtattatctggctgaataatatataattccgtttcgttattcagacatccaattatcttgatagattg-gattattgtcttt--cttatg-gttcagCATGGGGGCTGGATGTTCTCAACTCTTGTCTGACATGCAGGCTTTCAAG
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atttcactgcttatctgcatctacgatctaata----ggttctagacttatagttactattgggtaggcatttcatgatagttttctttaccttgtatgaccagTGTTGGTGCTGGATGCTCTCAACTCCTCTCTGATATGCAGGCTTTCAAG
upper sequence: AT5G55060.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0090g00690.t01 (Vitis vinifera), 3'ss of exon 8
aatagacgtattatctggctgaataatatataattccgtt-tcgttattcagacatccaattatcttgatagattggattattgtctttcttatggttcagCATGGGGGCTGGATGTTCTCAACTCTTGTCTGACATGCAGGCTTTCAAG
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gaagcaagtgtttcctctactaaagataaatattctttttgttgttcctttaatctaggcattctttgacaatttgtctcattttttcccctatg-ctcagTGTTGGTGCTGGATGTTCTCAACTACTTTCAGACATGCAGGCTTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcagacatccaattatcttgatagattggattattgtctttcttatggttcagCATGGGGGCTGGATGTTCTCAACTCTTGTCTGACATGCAGGCTTTCAAG
tcttgat putative branch site (score: 4)
ttattgtctttctt putative PPT
aattatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatagacgtattatctggctgaataatatataattccgtttcgttattcagacatccaattatcttgatagattggattattgtctttcttatggttcagCATGGGGGCTGGATGTTCTCAACTCTTGTCTGACATGCAGGCTTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA