Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgctaagtatctgcttcggagtcagatatttacatccaaattcacggatagcaaaatgtatgtggagggaaaatgtgaatgtatgttctggcatacatgatctctgtagatgcaattaacacgaaagttgatggtgtacagTATGATCGATCGCTTACACCGACCAAAAATATTGGACTGCCCGATTCATTGCTGTCACGATTTGACCTGCTTTTCATAGTGCTGGATCAAATGGATCCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S9_156V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S9_156V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA08G08920.1 (Glycine max), 3'ss of exon 8
gtaagtgctaagtatctgcttcggagtcagatatttacatccaaattcacggatagcaaaatgtatgtggagggaaaatgtgaatgtatgttctggcatacatgatctctgtagatgcaattaacacgaaagttgatggtgtacagTATGATCGATCGCTTACACCGACCAAAAATATTGGACTGCCCGATTCATTGCTGTCACGATTTGACCTGCTTTTCATAGTGCTGGATCAAATGGATCCAG
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-----------gtaagtggcattgtgagagaaatttgctgtgaagttta-aactaccaaagttcctg-------atattgt-actgaacctttatttat---ttttctaactagtggcttttattgtgcaattc-------tacagTATGATCGTTCATTGACTCCAACCAAAAATATCGGACTCCCAGACTCCTTGCTTTCTCGATTTGATCTACTTTTTATTGTGTTGGATCAAATGGATCCTG
upper sequence: PP1S9_156V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 8
gtaagtgctaagtatctgcttcggagtcagatatttacatccaaattcacggatagcaaaatgtatgtggagggaaaatgtgaatgtatgttctggcatacatgatctctgtagatgcaattaacacgaaagttgatggtgtacagTATGATCGATCGCTTACACCGACCAAAAATATTGGACTGCCCGATTCATTGCTGTCACGATTTGACCTGCTTTTCATAGTGCTGGATCAAATGGATCCAG
||| || | || |||| | || || | || |||| | || | | | ||| | | | | | | ||| ||| || ||| | || | ||||||||||||| || | || || ||||||||||||||||| || || || ||||| || |||||||| || || || || ||| | |||||||||||||| |
-----------gtaagtggcattatgcgggaaatttgctgtgaagttta-aactaccaaagttcctgatgttgtac----cgaacatttaattt----tttttcttctaaatagtggcttttattgtgcaattc-------tacagTATGATCGTTCATTGACTCCAACCAAAAATATTGGACTCCCAGACTCCTTGCTTTCTCGATTTGATCTACTGTTTATTGTGTTAGATCAAATGGATCCTG
upper sequence: PP1S9_156V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ25061 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtgctaagtatctgcttcggagtcagatatttacatccaaattcacggatagcaaaatgtatgtggagggaaaatgtgaatgtatgttctggcatacatgatctctgtagatgcaattaacacgaaagttgatggtgtacagTATGATCGATCGCTTACACCGACCAAAAATATTGGACTGCCCGATTCATTGCTGTCACGATTTGACCTGCTTTTCATAGTGCTGGATCAAATGGATCCAG
||| || || | | ||| | || | || | || | | ||| | | |||||||||||||| ||||| || || |||||||| || || || || || | |||||||||||||||||| | || || || || |||||||||||| |||
-------------------------------------------------------------------------------------gtaagtcttgacgca-atgctgggtgactaatcact---catggatgtttgt----tccagTATGATCGATCACTTACTCCTACAAAAAATATCGGGCTTCCGGACTCTCTACTGTCACGATTTGACCTGTTGTTTATTGTTCTTGATCAAATGGATGCAG
upper sequence: PP1S9_156V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ29981 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtgctaagtatctgcttcggagtcagatatttacatccaaattcacggatagcaaaatgtatgtggagggaaaatgtgaatgtatgttctggcatacatgatctctgtagatgcaattaacacgaaagttgatggtgtacagTATGATCGATCGCTTACACCGACCAAAAATATTGGACTGCCCGATTCATTGCTGTCACGATTTGACCTGCTTTTCATAGTGCTGGATCAAATGGATCCAG
||| || || | | ||| | || | |||| || | | ||| | | |||||||||||||| ||||| || || |||||||| || || || || || | |||||||||||||||||| | || || || || |||||||||||| |||
-------------------------------------------------------------------------------------gtaagtcttgacgca-atgctgggtgactaatcaat---catggatgtttgt----tccagTATGATCGATCACTTACTCCTACAAAAAATATCGGGCTTCCGGACTCTCTACTGTCACGATTTGACCTGTTGTTTATTGTTCTTGATCAAATGGATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctggcatacatgatctctgtagatgcaattaacacgaaagttgatggtgtacagTATGATCGATCGCTTACACCGACCAAAAATATTGGACTGCCCGATTCATTGCTGTCACGATTTGACCTGCTTTTCATAGTGCTGGATCAAATGGATCCAG
aattaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgctaagtatctgcttcggagtcagatatttacatccaaattcacggatagcaaaatgtatgtggagggaaaatgtgaatgtatgttctggcatacatgatctctgtagatgcaattaacacgaaagttgatggtgtacagTATGATCGATCGCTTACACCGACCAAAAATATTGGACTGCCCGATTCATTGCTGTCACGATTTGACCTGCTTTTCATAGTGCTGGATCAAATGGATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA