Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaacatcttcaagaggctgctagcttcagtgtcttgatgtccataaaatgttgcagttgattgtttttctatttttctattatgtctttgttgacaatattgtcaaatctggaatggtttctcagATTCGATATGGAGGATGCTATGATATTGAACAAATCATCAGTGGAGCGTGGCTTACACTATGGTCAAGTCTACAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S169_131V6.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S169_131V6.2 (Physcomitrella patens), 3'ss of exon 21
lower sequence: GLYMA13G26190.1 (Glycine max), 3'ss of exon 24
gtaagtaaacatcttcaagaggctgctagcttcagtgtcttgatgtccataaaatgttgcagttgattgtttttctattttt--ctattatgtctttgttgacaatattgtcaaatctggaatggtttctcagATTCGATATGGAGGATGCTATGATATTGAACAAATCATCAGTGGAGCGTGGCTTACACTATGGTCAAGTCTACAAG
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-------------------------------------------------gtaactgctttaatgcaaagcaactatagttttaaccatcctgtgctatttacaaatatcttgtgct----aactgttta-cagATATGATATGGAGGATGCTATGATTCTAAATAAGTCATCAGTGGAGCGTGGAATGTTTCATGGACAAATATATCAG
upper sequence: PP1S169_131V6.2 (Physcomitrella patens), 3'ss of exon 21
lower sequence: AT1G29940.1 (Arabidopsis thaliana), 3'ss of exon 21
gtaagtaaacatcttcaagaggctgctagcttcagtgtcttgatgtccataaaatgttgcagttgattgtttttctatttttctattatgtctttgttgacaatattgtcaaatctggaatggtttctcagATTCGATATGGAGGATGCTATGATATTGAACAAATCATCAGTGGAGCGTGGCTTACACTATGGTCAAGTCTACAAG
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----------------------------gtaagaaactgcttttgcgtacaagatcttgtcagtgataagcttt---tttcgttaatgtttcttctcttgttcttttatccacct---acctgtctcacagATTTGATATGGAAGACGCGATGATTTTGAACAAATCATCTGTGGAGCGGGGAATGTGCCATGGGCAAATATACCAG
upper sequence: PP1S169_131V6.2 (Physcomitrella patens), 3'ss of exon 21
lower sequence: Vv13s0084g00600.t01 (Vitis vinifera), 3'ss of exon 20
gtaagtaaacatcttcaagaggctgctagcttcagtgtcttgatgtccataaaatgttgcagttgattgtttttctatttttctattatgtctttgttgacaatattgtcaaatctggaatggtttctcagATTCGATATGGAGGATGCTATGATATTGAACAAATCATCAGTGGAGCGTGGCTTACACTATGGTCAAGTCTACAAG
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------------------------------------------------gtaaaa-attttagatgaatatgaagacatatatttcattttatagcatctgtatgattggttttttcgtaa--attatccagATACGATATGGAGGATGCTATGATTTTGAATAAGTCATCTGTGGATAGAGGGTTGTGTCATGGACAAATATACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttctattatgtctttgttgacaatattgtcaaatctggaatggtttctcagATTCGATATGGAGGATGCTATGATATTGAACAAATCATCAGTGGAGCGTGGCTTACACTATGGTCAAGTCTACAAG
tgttgac putative branch site (score: 3)
tttctc putative PPT
tctattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaacatcttcaagaggctgctagcttcagtgtcttgatgtccataaaatgttgcagttgattgtttttctatttttctattatgtctttgttgacaatattgtcaaatctggaatggtttctcagATTCGATATGGAGGATGCTATGATATTGAACAAATCATCAGTGGAGCGTGGCTTACACTATGGTCAAGTCTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG