Sequence
atgc intronic sequence ATGC exonic sequence...tttagtgaaagacttaaagtttcagttactgtgaaatcagtgctcaggagagtttgctatgctggttctcacatctctactttgtgattcttttctacagGACGATGATGATATAATAAATTCCTGGAACTTGCGAAAATGTAGTGCAGCTGGACTTGATATTTTATCAACTGTATTTGGAGATGAGATTCTTCCAGTTC
Basic information
species | Physcomitrella patens |
transcript | PP1S41_175V6.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S41_175V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------tttagtgaaag-acttaa---agtttcagttactgt-gaaatcagtgctcaggagagtttgctatgctggttctcacatctctactttgtgattcttttctacagGACGATGATGATATAATAAATTCCTGGAACTTGCGAAAATGTAGTGCAGCTGGACTTGATATTTTATCAACTGTATTTGGAGATGAGATTCTTCCAGTTC---
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gtatgttgtacttactctattgattgcttattctaattatttgattaattttcctgcccttatttaatagggtttgtgtagcttttgaaagatgaaatgataaaaatatgctttgctaattt--gaagtcaaattttatttttcatatttacagGATGATGATGTTGTCA---ACACATGGAATTTACGGAAATGCAGTGCAGCTGCTCTTGATATTCTTTCAAATGTGTTTGGAGATGAGATCCTTCCAACTCTTA
upper sequence: PP1S41_175V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------tttagtgaaag-acttaa---agtttcagttactgtgaaatcagtgctcaggagagtttgctatgctggttctcacatctctactttgtgattcttttctacagGACGATGATGATATAATAAATTCCTGGAACTTGCGAAAATGTAGTGCAGCTGGACTTGATATTTTATCAACTGTATTTGGAGATGAGATTCTTCCAGTTC---
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gtatgttgtactttctctattgattgcttattctaattatttgattaattttcctgcccttatttaatagggtgtgtgtagcttttgaaagaaggaatgataaaaaatgctttgctaattt--gaagtcaaactttatttttcctatttacagGATGACGATGTTGTCA---ACACATGGAATTTACGGAAATGCAGTGCAGCTGCTCTTGATATTCTTTCAAATGTGTTTGGAGATGAGATCCTTCCGACTCTTA
upper sequence: PP1S41_175V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 11
--tttagtgaaagacttaaagtttcagttactgtgaaa-tcagtgctcaggagagtttgctatgctggttctcacatctctactttgtgattcttttctacagGACGATGATGATATAATAAATTCCTGGAACTTGCGAAAATGTAGTGCAGCTGGACTTGATATTTTATCAACTGTATTTGGAGATGAGATTCTTCCAGTTC---
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aacctaatagtagtgttttttttcttctccttttaaaaacctgaggtttatatatttaatttttctggtt-----aactgta-ttggggacttattccatttacagGATGATGAAGCTGTCAATATTTGGAACTTGAGAAAATGCAGTGCAGCAGGTCTTGATATCCTTTCAGATGTGTTTGGGGATGAGATTCTTCCAACATTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggagagtttgctatgctggttctcacatctctactttgtgattcttttctacagGACGATGATGATATAATAAATTCCTGGAACTTGCGAAAATGTAGTGCAGCTGGACTTGATATTTTATCAACTGTATTTGGAGATGAGATTCTTCCAGTTC
ttctcac putative branch site (score: 2)
ttcttttctac putative PPT
attctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagtgaaagacttaaagtttcagttactgtgaaatcagtgctcaggagagtttgctatgctggttctcacatctctactttgtgattcttttctacagGACGATGATGATATAATAAATTCCTGGAACTTGCGAAAATGTAGTGCAGCTGGACTTGATATTTTATCAACTGTATTTGGAGATGAGATTCTTCCAGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG