Sequence
atgc intronic sequence ATGC exonic sequencegtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
Basic information
species | Physcomitrella patens |
transcript | PP1S46_53V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
-gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
||| | || | |||||| | ||| | || || || | | | | | || | || ||| ||| | | ||||||||||||||| | | |||||||| ||||| || |||||||| ||||| ||||||||||| || ||||||||||| | || ||||| || || ||||||
agtagg--atggttagtgacagggataatgcgagg--ggctgcaataaacgacttattttcaacattgacaaaagagaacttgaaaatttta--cctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
-------gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
||| | || | | ||| | | || | | ||| | || || ||| ||| | |||| | | ||||| || ||| || | |||||||||||||| ||||| || |||||||| ||||||||| | || |||||||| || | ||||| || |||||||| |||
ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgt-gcttcataatttga-----------cagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 5
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatat-cttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
||| || | | | || || | | || ||| || ||| | | | || | | | | | |||||| || || | | ||||| ||||| |||||||| ||||| |||||||||||||| || || || || || ||| ||||| | ||||| || ||||
------------------gtaaagatacatgtttcactcatcttcttctgcacttgcagttttcctaagcttatgtttccttttctgtaccatgcaacatgctcagGTAGACCGAGTTCTCTACTCTTCAGTCGTCTATCCTCACAACTATGGGTTCATTCCTCGCACGCTGTGCGACGATAGTGATCCTTTGGATGTGCTGGTCA
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 4
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgt--tggcttggctcaaccaccgctcctt--aatcttaacctca-tttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
|| | | | || | ||| || | | | | || ||| | | || | | || || || ||| | || ||| ||||||||||| || | |||||||||||||| || || ||||||||||| ||||||||| | ||||||||||| || | || || || ||||| | |||
-------tgtgttacataatttgtcaggatgattgagttct---gtgctgatgaaatgtaatagtttaatttgtttttctttctttctaacctttgctacaatttgacagGTTGATCGAGTCCTTTACTCATCAGTTGTATACCCTCACAATTATGGTTTCATTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTGGTCC
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G061928_T02 (Zea mays), 3'ss of exon 4
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctcctt--aatcttaacctca-tttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
|| | | | || ||| ||| | | | | | | | ||| || | || | || || | | | || ||| |||||||||| || |||||||||||||||| || || ||||||||||| ||| ||||| | ||||||||||| || | || || || ||||| | |||
-------tctgttacataatctgtcaggctgattcagtcctgaactgatgaaatg-taatggtttaatttgactttctttcgttctgacatgtgctacaatttgatagGTTGATCGAGTCCTGTACTCATCAGTTGTATACCCTCACAATTATGGTTTCGTTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTAGTCC
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 4
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
||| | ||| || | | ||| |||| | | | | | || || | | || | | |||||||||||||| | |||||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||| | |||||||| ||||| | || |
------------------------gtaatcatggttgcctagct-ttttcttcccttgttacacttgttgacaggatattgctgaacatgcatcta--tgtgcagGTTGATCGTATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTTATTCCACGTACTATTTGTGAGGACGGTGATCCCATGGATGTCTTGGTTA
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA10G05130.1 (Glycine max), 3'ss of exon 4
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
|| | | | || | || ||||| ||| || || | ||| | ||| | | || | | ||||||||||||||| | |||||||| ||||| ||||| ||||| |||||||| || ||||||||| |||||||||| | |||||||| ||||| | || |
--------------gtaatcatcgctgcctagttttttcttc---ccttgtcgcacttgttgctaca---ggatattgctgaacag-----gcatctatgtgcagGTTGATCGTATCCTTTACTCATCGGTTGTGTATCCTCACAACTATGGGTTTATCCCACGTACTATTTGTGAGGACGGTGATCCCATGGATGTCTTGGTTA
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 6
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
| | || | | | | | || ||| | | | | || || ||| || | ||| | || ||| | | |||||||||||||| ||||| |||||||||||||| || ||||||||| |||||||||| |||||| | ||||| | | |
------------------------------gttgcaatcgttgcagagttattttttattatattgttactatgtcaagttctaaacactaatcta--tgaacagATCGACCGTGTTCTTTACTCATCAGTTGTGTATCCTCACAATTATGGGTTTATCCCACGTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTA
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA19G35710.1 (Glycine max), 3'ss of exon 6
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
| ||| | | || || || ||| || || | || | || | | || || ||| || | ||| | || || | | |||||||||||||| ||||| ||||| |||||||| || || |||||| |||||||||| |||||| | ||||| | | |
---------------------gttgtaatagttgctgagtt---attttc--gattctacggtt--actaagtcaa-gttgctaaacactaatcta--tgcacagATCGACCGCGTGCTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTTATCCCTCGTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTA
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA01G37790.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------------------gtacgtcattgccagtgactaactctaaacgatcttgtcttca-tatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
| | ||| || | || | || ||| || || | || || | | || || | || | ||| | ||| | | | | ||||||||||||| | ||||||||||||||||| |||||||| ||||| || || ||| | || ||||||| || ||||| || || || || ||
gtgtcgtttccattttctttcttgcactcctcttcttccattccatatgcttaatgtattagcaaaatgtgaaagactttcttttaatagggcagtattctcatttaccatttccaaatttatttctcattgctacctgtctgtggtga-agcataactaactcactaacgaatgttctgatcaacccaacttagGTTGATCGTATTCTTTACTCATCAGTTGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTC
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggct-caaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
| ||| | || ||| || | ||| | | || || || | || | | | | ||| | | | |||||||||||| | ||||||||||||||||| ||||| || || ||||| ||||| ||| | ||||| ||||| || | ||||| |||||||| | ||
-----ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccatta-ctcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------gtacgtc---attgccagtgactaactctaaac--gatcttgtcttcat--atcttcacga-gctgttggcttggctcaaccaccg----ctccttaat-------cttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
||| | | | | |||| || | || ||| | | |||| | | | ||| | | || || || || || ||| ||| || | | | | ||||||||||||| | ||||||||||| ||||| |||||||| ||||| || || ||| | || ||||||| || ||||| || || || || ||
gtgtggttgccattttcttgcattcctcttcttcatttccttatgcttgatgtatttgcaaaatatgaaagactttcttttaataggatagtattctcatttaccatttcgaagtttatgtctgtactgaagcataactaactcactaacgaatgtgctgatcaacccaacttagGTTGATCGTATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTC
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
|| || |||||| | ||| | | ||||| | |||| | ||||| ||| | | | || | || | |||| |||||| || ||||||||||| || ||||| |||||||||||||| || ||||| ||||| || | ||||| || | ||||| ||||||| || |||
----gtaat-----gtgact--tcccaaagattgtgatcttcttttctttt--aactgttctgatggatga---------cattgaatttgatctca-------gGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgtcattgccagtgactaactctaaacgatcttgtcttca-tatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
| |||| ||| || | | ||||| | | || || | || | ||| ||| || || |||||| || ||||| | |||||||| || || || |||||||| |||||||||||||| ||||| ||||||||||| || || ||||||||||| ||||
----------------------gtataaatttgattgcattaactttcttcgctgtccctttcattattagaggtacgattgtctaaactttacacatattctcagGTCGACCGTATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCA
upper sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 4
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
||| | | | ||| || ||| | | | | || || || | ||||| | | | ||| || | | | | |||||||| ||| | ||||||| |||||||| || || ||||| ||||| || || ||||||||||| |||||||| | || ||||| ||||| | || |
------------------gtaatt--aggtgttctaatc--catttttctaggtactctttgc--agatcaacaattggttgctaaattttatattcatgtgcagGTTGACCGTGTGCTGTACTCTTCAGTTGTGTACCCCCACAACTATGGCTTTATCCCACGTACTCTCTGTGAGGACAATGACCCCATGGATGTCTTGGTTAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|208349328|gb|DC910387.1|DC910387EST: AGGGAAGTAAGGTAAAGTACGAACTTGACAAGAAAAGTGGTCTCATGAAG GTTGATCGTATCNTGTACTCATCANNTGTCTATCCACACAATTATGGGTTC
genomic: AGGGAAGTAAGGTAAAGTACGAACTTGACAAGAAAAGTGGTCTCATGAAGgtacgtcatt ... catttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
tcttaac putative branch site (score: 2)
cctcatttttc CT-rich tract
ttaatcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT