Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcatgaaccggaaattgcgaggttttgtgaggatcgaaaacagatcacgagacttcgaactttaagacgtcttttttgaagatttttgaagatttacgtctaaggttgatttacagtcattcactgatcatctaccttcagcaagggttcttactaattagttggctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACCAA
Basic information
species | Physcomitrella patens |
transcript | PP1S150_142V6.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S150_142V6.1 (Physcomitrella patens), 3'ss of exon 24
lower sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 22
gtaagttcatgaaccggaaattgcgaggttttgtgaggatcgaaaacagatcacgagacttcgaactttaagacgtcttttttgaagatttttgaagatttacgtctaaggttgatttacagtcattcactgatcat-ctaccttcagcaagggttcttactaattagttggctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACCAA
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-------------------------------------------------------------------------------------------gtcggtattaactggcagagcacatctat--ttgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttc-cttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA
upper sequence: PP1S150_142V6.1 (Physcomitrella patens), 3'ss of exon 24
lower sequence: EFJ33165 (Selaginella moellendorffii), 3'ss of exon 22
gtaagttcatgaaccggaaattgcgaggttttgtgaggatcgaaaacagatcacgagacttcgaactttaagacgtcttttttgaagatttttgaagatttacgtctaaggttgatttacagtcattcactgatcatctaccttcagcaagggttcttactaattagttggctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACCAA
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----------------------------------------------------------------------------------------------------------------------------gtattattgtaacctgtgtttc-caggttttctgacccggaa-----ttgctgacagGCGCGACTCTTCTTCCATCATCCGAAGTTTGGAATTCTGGACGAATGCACCAA
upper sequence: PP1S150_142V6.1 (Physcomitrella patens), 3'ss of exon 24
lower sequence: EFJ22756 (Selaginella moellendorffii), 3'ss of exon 23
gtaagttcatgaaccggaaattgcgaggttttgtgaggatcgaaaacagatcacgagacttcgaactttaagacgtcttttttgaagatttttgaagatttacgtctaaggttgatttacagtcattcactgatcatctaccttcagcaagggttcttactaattagttggctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACCAA
| | | | || || || | |||| || | || |||||| ||||| |||||||||||||| |||||||||||||| ||||| ||||||||
----------------------------------------------------------------------------------------------------------------------------gtattattgtaacctgtgtttc-caggttttctgacccgg-----gattgctgacagGCGCGACTCTTCTTCCATCATCCGAAGTTTGGAATTCTGGACGAATGCACCAAMapped 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|162229424|gb|FC404783.1|FC404783EST: CCAATTGGGAGGACATGCTCTCGCTTGGAGAGCAGCAAAGGCTTGGAATG GCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACC
genomic: CCAATTGGGAGGACATGCTCTCGCTTGGAGAGCAGCAAAGGCTTGGAATGgtaagttcat ... ctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACC
EST:
gi|162229425|gb|FC404784.1|FC404784EST: CCAATTGGGAGGACATGCTCTCGCTTGGAGAGCAGCAAAGGCTTGGAATG GCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACC
genomic: CCAATTGGGAGGACATGCTCTCGCTTGGAGAGCAGCAAAGGCTTGGAATGgtaagttcat ... ctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACC
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:
25 (upstream exon),
28 (downstream exon)
Score:
2TGTGAGGTTGGTTTACCTGCTGGACCGGGAAGGGGGATGGGATGCTACTGCCAATTGGGAGGACATGCTCTCGCTTGGAGAGCAGCAAAGGCTTGGAATGgtaagttcat ... ctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACCAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcactgatcatctaccttcagcaagggttcttactaattagttggctgtcaacagGCACGACTATTCTTCCATCATCCCAAGTTTGGAATTCTTGACGAGTGCACCAA
tactaat putative branch site (score: 2)
ttactaatta TA-rich tract