Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgtcttacgaatctcattgtgtaaatgatggcttctgaagttcgtgatattgtccgttttatcgcttgcattaggacgtgattactttagcaagtcactgaggcgtgttgtattggctacgagaagttgcaagagttggaacggtgttttaacaggcttgggtttttgtggcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAAGTTCTG
Basic information
species | Physcomitrella patens |
transcript | PP1S60_100V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 6
gtacgtgtcttacgaatctcattgtgtaaatgatggcttctgaagttcgtgatattgtccgttttatcgcttgcattaggacgtgattactttagcaagtcactgaggcgtgttgtattggctacgagaagttgcaagagttggaac-ggtgttttaacaggcttgggtttttgtggcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAAGTTCTG
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--------------------------------------------------------------------------gtatagtagtaatttctgtttgaattcattaaggagaaattcatc--tttagttaaattataagcgcagcttcagatggtttaatgcaattc--tatttgtgcaacagGTTAATCCTCATACCCATCAGCTAAAATTGTGTGACTTTGGCAGCGCGAAAGTTCTG
upper sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 5
gtacgtgtcttacgaatctcattgtgtaaatgatggcttctgaagttcgtgatattgtccgttttatcgcttgcattaggacgtgattactttagcaagtcactgaggcgtgttgtattggctacgagaagttgcaagagttggaacggtgtttta-acaggcttgggtttttgtg-gcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAAGTTCTG
|| || || || | || ||| || || || |||| | |||||| ||||||||||| || || ||||| || |||||||| |||||||||||||| |||
---------------------------------------------------------------------------------------------------------------------------gtaggaggtccttgtcctttgagggttgatttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGACTTCGGCAGCGCCAAAGTGCTG
upper sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
gtacgtgtcttacgaatctcattgtgtaaatgatggcttctgaagttcgtgatattgtccgttttatcgcttgcattaggacgtgattactttagcaagtcactgaggcgtgttgtattggctacgagaagttgcaagagttggaacggtgttttaacaggcttgggtttttgtg-gcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAAGTTCTG
|| || || | | | ||| || || || |||| | |||||| ||||||||||| || || ||||| || ||||| ||||||||||||||||| |||
---------------------------------------------------------------------------------------------------------------------------gtaggaggtccttgtccttaggattg-atttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTGMapped 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|162249128|gb|FC420379.1|FC420379EST: ATAACGGCATTGGTGTGTGTCACCGAGACATCAAGCCACAGAACCTGCTG GTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAA
genomic: ATAACGGCATTGGTGTGTGTCACCGAGACATCAAGCCACAGAACCTGCTGgtacgtgtct ... tgtggcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAA
EST:
gi|162165971|gb|FC341802.1|FC341802EST: ATAACGGCATTGGTGTGTGTCACCGAGACATCAAGCCACAGAACCTGCTG GTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAA
genomic: ATAACGGCATTGGTGTGTGTCACCGAGACATCAAGCCACAGAACCTGCTGgtacgtgtct ... tgtggcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAA
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:
28 (upstream exon),
33 (downstream exon)
Score:
14ATACGTAAAGTTGTACACTTATCAGATCTGCCGGTCTTTGGCGTATATTCATAACGGCATTGGTGTGTGTCACCGAGACATCAAGCCACAGAACCTGCTGgtacgtgtct ... tgtggcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAAGTTCTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaagttgcaagagttggaacggtgttttaacaggcttgggtttttgtggcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAAGTTCTG
ttttaac putative branch site (score: 14)
tttttgt putative PPT
tgttttaa TA-rich tract