Sequence
atgc intronic sequence ATGC exonic sequencegtgggattgctttgaaacgttatgatagtgtcatgtatatgaagttgctgaaacccttgggactctttgtgtatacactgattctatttggctccgatggagagtccaagtctaactttgatcccacgattataattttccatggtcggtagTCTGGAACGCCTTCAACCGGTAAGACGATTGCGACGCAGTTTGATGCATGTGCAAGCTGGTGGACTCAAGGCCCTGATTCTATCTTGCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S68_291V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S68_291V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os08g14770.1 (Oryza sativa), 3'ss of exon 3
gtgggattgctttgaaacgttatgatagtgtcatgtatatgaagttgctgaaacccttgggactctttgtgtatacactgattctatttggctccgatggagagtccaagtctaactttgatcccacgattataattttccatggtcggtagTCTGGAACGCCTTCAACCGGTAAGACGATTGCGACGCAGTTTGATGCATGTGCAAGCTGGTGGACTCAAGGCCCTGATTCTATCTTGCAG
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----------------------------------------------------------------gtttgccaagcatctaggactattttg-taaaaaggaaaattatgatgaaaatctaatagaattttagttacattgt-tgctcattcttttggtgcagGTTAAA--GACAAAACGATTGTTCCCCAGTTTGATGCATGTGCTAGTTGGTGGACACAAGGACCTGATTCTAACTTACAG
upper sequence: PP1S68_291V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G102156_T01 (Zea mays), 3'ss of exon 3
gtgggattgctttgaaacgttatgatagtgtcatgtatatgaagttgctgaaacccttgggactctttgtgtatacactgattctatttgg-ctccgatggagagtccaagtctaactttgatcccacgatta---taattttccatggtcggtagTCTGGAACGCCTTCA--------ACCGGTAAGACGATTGCGACGCAGTTTGATGCATGTGCAAGCTGGTGGACTCAAGGCCCTGATTCTATCTTGCAG
| ||| | | | ||| ||| | |||| || | | || | | | | | |||| | | | | | ||| | | ||| || | || | | | || | | | | || ||||||||||| ||||| |||||||||||||| |||||||||| |||||||
-----------------------------------------------------gtttgtccactttctagttctactctgtcttcattttttcttcaaaagaaatttgtaatgaagttttggttgtgcagcaaggttggctgaacattatattgattctctaaatctttgatgtagATTAAAGACAAAATGCTCATCCCTCAATTTGATGCATGCGCAAGTTGGTGGACTCAAGGGCCTGATTCTAACTTGCAG
upper sequence: PP1S68_291V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 3
gtgggattgctttgaaacgttatgatagtgtcatgtatatgaagttgctgaaacccttgggactctttgtgtatacactgattctatttggctccgatggagagtccaagtctaactttgatcccacgattataattttccatggtcggtagTCTGGAACGCCTTCAACCGGTAAGACGATTGCGACGCAGTTTGATGCATGTGCAAGCTGGTGGACTCAAGGCCCTGATTCTATCTTGCAG
| ||| | | || | ||| || | | ||| || | || | ||| || | |||||| | | || ||| | | || || | || |||||||||||||| ||||||||||||||||| || ||| |||| |||||
---------------------------------------------------ggttttatggaattacttcgttcatacttctttatatgtattttgatattgacacagagatttttttttgcttcatcttgtgaattttttttag------gttcagAAGACA----------GAAGTCATAGCACCACAATTTGATGCATGTGCTAGCTGGTGGACTCAAGGACCCGATGCTATAATGCAG
upper sequence: PP1S68_291V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 3
gtgggattgctttgaaacgttatgatagtgtcatgtatatgaagttgctgaaacccttgggactctttgtgtatacactgattctatttggctccgatggagagtccaagtctaactttgatcccacgattataattttccatggtcggtagTCTGGAACGCCTTCAACCGGTAAGACGATTGCGACGCAGTTTGATGCATGTGCAAGCTGGTGGACTCAAGGCCCTGATTCTATCTTGCAG
| | | | | |||||| | | | || | | | | | || | || | | || | | || | |||| ||| | | | | | | | | ||||| ||||||||||||||||| || |||||||||||||| |||||| | | ||||||
-------------------------------------------------------caggtagatacatat-tatacaatacattt-cttaatggtgctataaa-tacagatgcaattgtattctga--acta-attttttcattttttatgtccaatatagGTCCAGAATAATGATTTCATTGCACAACAGTTTGATGCATGTGCTAGTTGGTGGACTCAAGGACCTGATGCCACTTTGCAG
upper sequence: PP1S68_291V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ22227 (Selaginella moellendorffii), 3'ss of exon 3
gtgggattgctttgaaacgttatgatagtgtcatgtatatgaagttgctgaaacccttgggactctttgtgtatacactgattctatttggctccgatggagagtccaagtctaactttgatcccacgattataattttccatggtcggtagT-CTGGAACGCCTTCAACCGGTAAGACGATTGCGACGCAGTTTGATGCATGTGCAAGCTGGTGGACTCAAGGCCCTGATTCTATCTTGCAG
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-------------------------------------------------------------------------------------------------------gtttgtattatactgctttcttttagttgcgtactgacttttcaaactgtgccagAATAAACACGGCCGCT-------TTGCTCAGCAGTTTGATGCTTGTGCAAGCTGGTGGACGCAGGGGCCCGATGCATCACTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggagagtccaagtctaactttgatcccacgattataattttccatggtcggtagTCTGGAACGCCTTCAACCGGTAAGACGATTGCGACGCAGTTTGATGCATGTGCAAGCTGGTGGACTCAAGGCCCTGATTCTATCTTGCAG
ttttccat CT-rich tract
attataattttccat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggattgctttgaaacgttatgatagtgtcatgtatatgaagttgctgaaacccttgggactctttgtgtatacactgattctatttggctccgatggagagtccaagtctaactttgatcccacgattataattttccatggtcggtagTCTGGAACGCCTTCAACCGGTAAGACGATTGCGACGCAGTTTGATGCATGTGCAAGCTGGTGGACTCAAGGCCCTGATTCTATCTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA