Sequence
atgc intronic sequence ATGC exonic sequence...tggatctattttgagattttaatcaggattgattttggtgagatgcatgcgaaagcttcaattaggaggcgtgctcacagcttttatggttttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGTTTCCGAGTTAAGG
Basic information
species | Physcomitrella patens |
transcript | PP1S227_48V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S227_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
----tggatctattttgagattttaatcaggattgattttggtgagatgcatgcgaaagcttcaattaggaggcgtgctcacagcttttatggttttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGTTTCCGAGTTAAGG---
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gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgtt--gactctctcttatgtgtgttttgttctt----tagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTCGAGTGGTCAGCATG
upper sequence: PP1S227_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
----------------------------------------------tggatctattttgagattttaatcaggattgattttggtgagatgcatgcgaaagcttcaattaggaggcgtgctcacagctt----ttatggtt-ttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAA-AGCTCGGATG-GTTTCCGAGTTAAGG
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gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA--
upper sequence: PP1S227_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
----------------tggatctattttgagatttta--atcaggattg-attttggtgagatgcatgcgaaagcttcaatta--ggagg-----cgtgctcacagcttt---------tatggttttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGT--TTCCGAGTTAAGG
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gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactattcatttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgcgaaagcttcaattaggaggcgtgctcacagcttttatggttttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGTTTCCGAGTTAAGG
tgctcac putative branch site (score: 2)
ttcaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggatctattttgagattttaatcaggattgattttggtgagatgcatgcgaaagcttcaattaggaggcgtgctcacagcttttatggttttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGTTTCCGAGTTAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA