Sequence
atgc intronic sequence ATGC exonic sequence...attcatggtacctgaattggatggttcagggaaatgattggatacttctttaatgatttttttttgtcaattgttcactttgtggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
Basic information
species | Physcomitrella patens |
transcript | PP1S113_117V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 6
attcatggtacctgaattggatggttcagggaaatgatt---ggatacttctttaa--tgatttttttttgtcaattgttcactttgtggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
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-----------------------gtttgaaaatatattttttaaattcttccttcaactaaggtatcactgctagttactgaacttataaa---tgatgatgcagGTGCTAAATCAGGATGAGACACCTTTGCTGTACAGTCTTGTATTTGGGGAGGGTGTTGTGAATGATGCTACATCAGTGGTGCTTTTCAATGCAATCCAAA
upper sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 6
attcatggtacctgaattggatggttcagggaaatgattggatacttcttt--aatgatttttttttgtcaattgttcactttgtggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
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------------------gtttgaagcaatatatttttaaaattcttccttcaactaaggtatcactgctagttactgaacttataaa---tgatgatgcagGTGCTAAATCAGGATGAGACACCTTTGCTGTACAGTCTTGTATTTGGGGAGGGTGTTGTGAATGATGCTACATCAGTGGTGCTTTTCAATGCAATCCAAA
upper sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 5
attcatggtacctgaattggatggttcagggaaatgattggatacttctttaatgattttttt------ttgtcaattgttcactttg---tggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
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-----------------------gtttggaacaatatgtgcctttttccgcaacgttgcagcaaccaaggtgtcaatgcttagtactgaacttataaatgatgttgcagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTGGTGCTTTTCAATGCAATCAAAA
upper sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 2
attcatggtacctgaattggatggttcagggaaatgattggatacttctttaatgatttttttttgtcaattgttcactttgtggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
||| ||| | || ||| | | | | | | | | | || ||| || || ||| | ||||| |||||||| |||||||| ||| ||||||||||| | || |||||||| || || || |||||||| || ||||| || || || ||| ||||
-------gtaatgtgattcgccaattagcagaagtacatacaggcc-cagaatcaaagtgtaattaacaaaaactcttgttcc----tttggtgatacagGTTCTCAATCAAGATGAGACACCTTTGCTTTACAGTCTTGTATTTGGAGAGGGCGTTGTGAATGATGCCACATCTGTTGTGCTCTTCAATGCTATTCAGA
upper sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 5
attcatggtacctgaattggatggttcagggaaatgattggatacttctttaatgatttttttttgtcaattgttcactttg--tggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
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---------gtatagatatctt--ctcaaggctgtgattc--tgcttccataatggggacaatagaacattt-ctgactaaagtttgcatctgatatggcagGTGCTCAATCAGGATGAGACACCTTTGCTATACAGTCTAGTCTTTGGGGAAGGTGTGGTAAATGATGCCACATCTGTG----------------------
upper sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 6
attcatggtacctgaattggatggttcagggaaatgattggatacttctttaatgatttttttttgtcaattgttcactttgtggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
|||| | ||| | | | |||| || | | | || | | | ||| | | |||||||||| |||||||||||||| || | || |||||| |||| ||||||||||| || || |||||||| || |||||||| || || || | ||
-------gtac---agatggccttactaagctgtgatcctgttactagttctaagggacaacact-tccacaactta-tttatccaatccaattgtgcagGTGCTTAATCAGGATGAGACACCCTTACTCTACAGTCTGGTTTTTGGAGAAGGTGTTGTGAATGATGCCACATCTGTGGTGCTTTTCAATGCAATCCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttaatgatttttttttgtcaattgttcactttgtggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
ctttaat putative branch site (score: 4)
cttgtcttt putative PPT
taatgatttttttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcatggtacctgaattggatggttcagggaaatgattggatacttctttaatgatttttttttgtcaattgttcactttgtggtgcttgtctttgcagGTGCTCAATCAGGATGAGACCCCTCTGCTTTACAGTTTGGTGTTTGGAGAAGGAGTAGTCAATGATGCTACTTCTGTGGTTCTATTTCGGGCTGTTCAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT