Sequence
atgc intronic sequence ATGC exonic sequencegtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
Basic information
species | Physcomitrella patens |
transcript | PP1S230_93V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 2
gtacagattatgg-ctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
||| |||| ||||| | || | || || | | || | | || | | | |||| | || | | || || | || | |||| ||| | | | | | | ||| || || || |||| ||||| ||||||||||| || || | |||||||| ||||||||||| || ||||||||||| | || ||||| ||||||||||| || ||||| |||||
--gtagactatgaactata--------tcacctgccctttgtaacttgttatccc-----ctgaacctactattttaccaatg-------acaggctactgttttcattccacacatgtttaaatttcat-------aatttcaattgattttaacctatgcctcgtgctgg-----tgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
||| ||| | ||| | || | |||| | | | | | || | ||| |||| || | | | | | ||| ||| | || | ||| | | ||| | || | | ||| | || |||| || |||| ||||||||||| || || | |||||||| | ||||||||| || ||||||||||| | || ||||| ||||||||||| || ||||| || ||
--gtagaccatgaatcctattgtatgcagtttgcaacttgttatcccctgaacctactattttag-cggtgacaggctactgttttcttttcac-----acctgtttaaatttcataatt-----tcagtgacaattttcat-ctcagttttaacatatgcttct---tgtgctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATTGTGAAGCTGCTTGATATTGTTAGAGATCAGCATTCAAAAACACCAAGCT
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtca-gtgttttgcta--aagtctccatatagtctgcaagttgtggcgattatgc-agttaatttttgt--tgagagtattcttgttc-----tgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
| ||| | ||| || | | | || |||| | | | | || || | |||| || ||| | | | | | | | ||| | | || ||| ||| ||| || | ||| | ||| | | || | |||| |||| ||||| || ||||| ||| | |||||||| |||||||| || || ||||||||| | | || ||||||||||||||||| || || || ||||||
----------------------gtacttgaaggaatatgctgccttttctttgcaacattttcccttgcacattctgttttcaagtgaatttacagttttgatgata-gaagttggtgccaaagagttactgtcatgaacgtagtcatcttcatggtgggtcttttaacatacccttcatatgtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATTGTGAAGTTGCTTGATATTGTCAGAGATCAGCATTCAAAGACTCCCAGTT
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtct-gcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
| ||| |||| || || | || | ||| | || | || || || | ||| | | ||| | | || | ||| | | || ||||||||||||| || || ||| | |||||| | ||||||||||| |||||||| |||||| | || |||||||||||||| || || ||||| ||||||
------------------------------------------------------------------tgttaattttttaaa--ctttattttgtttagcatactatgccattt-------caaattcttctgatatttttccttactttatgcactcttcaatatta-------ttttacagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGTGGAGGCCCAAATATTGTCAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G22250.1 (Glycine max), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
||| | || | || | || || | | | |||| | | || |||| |||| || |||| | | || ||| | | | || ||||||||||||| || || ||| | ||||| || ||||| ||||| |||||||| |||||| | || ||||||||||||||||| || ||||| || ||
-------------------------------------------------------------------------ttgattttgtttttggtta-tatggtgtttcttgtactactgcattcagttcttgt-gaga---tttttgtctt-acct--tctgagatcttcaacatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAACCTTTGTGGTGGCCCAAATATTGTCAAGCTTCTTGATATTGTCAGAGATCAGCACTCTAAAACTCCTAGCT
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
| |||| |||| | | | | | | || | || || || | ||| | | | || || | | | |||| | | || ||||||||||||| || || ||| | |||||| | || |||||||| |||||||| |||||| | || |||||||||||||| || || ||||| ||||||
------------------------------------------------------------------tgttatttttttaaaacttattt-tgtttcacgtactatgccattt-------caaattcttctgatatt--ttttattactttatgagctct-----tcaatatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G17520.2 (Glycine max), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
| | | | | ||||| | | | | ||| | || | | | | | | | | | ||||| |||| ||||| |||| ||| || || |||||||| |||||||||||||| |||||||| || ||| |||| ||| | | |||||||| ||||| |||||||| || ||||| ||||
-----------------------------------------------------------------------atatatatatatatatatata-tatatatatatatatatatatatatata-tatatatatatataaatgtaactctgacaatgcttctgtttctgaatgca--------gATCAAGAGGGAAATCAAAATATTACAGAATCTTTGTGGAGGGCCTAATGTTGTAAAGTTGCTTGACATTGTTAGAGACCAGCAATCGAAGACCCCAAGTC
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcga-ttatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
| | | | | | | || ||||| | || || | |||| |||| |||| || |||| | | | || | | | || ||||||||||||| || || ||| | ||||| || ||||| || || |||||||| |||||| | || ||||||||||||||||| || ||||| || ||
---------------------------------------------------------------------------atttgaatttattttttggttgtttgttgtactaacttcagctttcaattcttgt-gaga---tttttgtcataactt---ctgagatcttcaacatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAACCTTTGTGGGGGGCCAAATATTGTCAAGCTTCTTGATATTGTCAGAGATCAGCACTCTAAAACTCCTAGCT
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G22320.1 (Glycine max), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
|||| ||| | | | || | | || || || | || ||| | | | | | | || |||||| | | | |||| || || |||||||| |||||||||||||| |||||||| || |||||||| || | | |||||||| ||||| || || || || ||||| ||||
---------------------------------------------------------------------------gcta---tctagttgtttattttaaagtataataatgattgtcttccatccctctggttatatatatatgtaactttga-caatgattctggttctgaatgc--agATCAAGAGGGAAATCAAAATATTACAGAATCTTTGTGGAGGGCCTAATATTGTACAGTTGCTTGACATTGTTAGAGACCAACAGTCGAAGACCCCAAGTC
upper sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 2
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
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-----------------------------------------------------------ttgcggtaaatttt---cccaggtttctatgggaattcttattactggca--tattccattgacttttc----agatatcagtgcaac------atatttacttctg-------ttttgcagATAAAGAGGGAGATAAAAATACTTCAGAACCTTTGTGGAGGCCCAAATATTGTGAAGCTGCTTGATATTGTCAGAGATCAGCATTCCAAAACTCCTAGCTMapped 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|100424237|gb|BY958384.1|BY958384EST: ACAATGAGCGTTGCGTGATCAAAATTTTGAAGCCTGTCAAGAAGAAAAAG ATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATT
genomic: ACAATGAGCGTTGCGTGATCAAAATTTTGAAGCCTGTCAAGAAGAAAAAGgtacagatta ... atcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATT
EST:
gi|100381374|gb|BY950096.1|BY950096EST: AATGAGCGTTGCGTGATCAAAATTTTGAAAGC-TGTCNNAGA-GAANNAG ATTNAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCCATATT
genomic: AATGAGCGTTGCGTGATCAAAATTTTGAA-GCCTGTCA-AGAAGAAAAAGgtacagatta ... atcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
32 (upstream exon),
34 (downstream exon)
Score:
6GGTGGGGCGCGGCAAATACAGCGAGGTGTTTGAAGGTGTCAATATTGTTAACAATGAGCGTTGCGTGATCAAAATTTTGAAGCCTGTCAAGAAGAAAAAGgtacagatta ... atcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
atctaat putative branch site (score: 6)
catcttctt putative PPT
tattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagattatggctatagttgggactgacaagaaattggttagtcattttggcaaaagctacagtcagtgttttgctaaagtctccatatagtctgcaagttgtggcgattatgcagttaatttttgttgagagtattcttgttctgatctaatctctggttctggctgcatcttcttagATTAAAAGAGAAATCAAGATATTACAGAATCTGTGTGGAGGCCCCAATATTGTGAAGCTTTTGGACATTGTCAGAGATCAGCAATCCAAAACCCCCAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA