Sequence
atgc intronic sequence ATGC exonic sequencegtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
Basic information
species | Physcomitrella patens |
transcript | PP1S22_429V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os12g19290.1 (Oryza sativa), 3'ss of exon 5
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgaca--caaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
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------------------------------------------------------------------------------gtcgatagaaaattgtagaaaaaatggca--tggtaatcatttgtttgccaaagagccttggcagtgtgttttttatgtatttactttcatgataattgcagGCTTATTCAACAGTTGGTACACCTGATTACATTGCTCCGGAGGTACTATTGAAGAAAGGATATGGAATGGAGTGTGACTT
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 6
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
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-----------------------------------------------------------ttatagtattttgggt---atctatatgaat--------ggtgtttaagatagtgttcttcgacatcttttt--tttgagtgcttgtaatttttgaatgtgtaaacattg------cagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctcc-atgatgttctactactctttgagcatctagttttcaggttttga-cacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
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----------------------------------------------------------------------------ttcattatac-tattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgt---gtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 5
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatcta-gttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
|| || || | || || |||| || ||| | | | | | | |||| | | | | | | | | | || |||| || | ||| | | || | || | | | | | | ||||||||||| || || || || ||||| ||||| ||||| ||||| || ||||| ||||||||||||||||| ||||| ||
-----------------------------gtaagttaattactattatgtagaggtttgttttt-tgtttattatgatagt-gagtgtaat---tgtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT2G20470.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
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-----------------------------------------------------------------------------------------------gtaag-gcttcatattcacctttgagattttcaa-tagagtttctccctctgtgtgtgtctgattaacacatg-tcacgacagGCTTATTCCACAGTTGGCACACCAGATTACATAGCTCCAGAAGTTCTGTTGAAGAAAGGCTATGGGATGGAGTGTGACTG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtat---acattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
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--------------------------------------------------------------------------catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggacttt------atttttttctgtaatgttcatattcgaacttg-cagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatg--taggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
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-------------------------------------------------------------------------gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgt-----tttgtatttatagttctgtcatatgctatc--tagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
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------------------------------------------------------------------------------------------------------------------gtgcgtagc-ttgtacttccttttgt---cccgattttta--tctaagtgtt---ctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG
upper sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttc---aacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
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------------------------------------------------------------------------------------------------------------------------------gtgcgtagcttgtacttccttttgtcccgatttttatctaagtttcctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
ttttgac putative branch site (score: 3)
tagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA