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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattttcagtattgcgcttctcggtttttttgaattaaaggagacagaccatgtataccaatgaaccacctagtttaagagatcccagtgatttttcattgtgatcttacatacttgtacgacgttttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCT

Basic information

species Physcomitrella patens
transcript PP1S37_351V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
---------------------------------------------------gtaaattttcagta-ttgcgcttctcggtttttttgaattaa---aggagacagaccatgtataccaatgaaccacctagtttaagagatcccagtgatttttcattgtgatcttacatacttgtacgacgttttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCT
                                                    ||||     || |  ||| ||| |   | ||||   |  |        ||||||  ||  |||      || ||| |  |||      | |   | | || || || |||||||||||   | |      | |    ||||| ||||| || || || || ||||| ||||||||||| ||| |||| |||||||| || || ||||||||| | |||||||| ||||| || || ||  |
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttt-tgttttcacaccagcctgcatgacagattataaata-----aaaacactttttttgttttcttcttattagttatc-ttatgatcttacatgtattt------tctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT

upper sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
gtaaattttcagtattgcgcttctcggtttttttgaattaaaggagacagaccatgtataccaatgaaccacctagtttaagagatcccagtgatttttcattgtgatcttacatacttgtacg--acgttttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCT
            ||    | |  |    |||| | |    ||    | || |    |       |  |  | ||  |||  | | |  |  |  || ||  | || ||||||    |||  | |  |  | |    ||||| ||||| || || || || ||||| ||||||||||| ||| |||| |||||||| || || ||||||||| | |||||||| ||||| || || ||  |
----------gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttc--ttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT

upper sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaattttcagtattgcgcttctcggtttttttgaattaaaggagacagaccatgtataccaatgaaccacctagtttaagagatcccagtgatttttcattgtgatcttacatacttgtacgacgttttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCT
                                          | ||    |  | | ||||||||  |    || |   ||   |||    ||  ||     | |||    |||  ||  || ||   | |    |||| | ||| ||| | || || |||||  | |||||||| ||| |||| |||||||| || || || |||||||| ||||| ||||| || |||||||||||
------------------------------------------gtaggtttagtaagaataccaattcaatgtctcga--aaagaatcattttggattccttgtttgac---aca-gctcttatgataatct---tcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT

Mapped 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|37851230|gb|BJ609238.1|BJ609238
EST:     AATTTCAGTTCCGCTTGCATTACAG                         GTACTGCGCNTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGG
genomic: AATTTCAGTTCCGCTTGCATTACAGgtaaattttc ... tttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGG
EST: gi|37853461|gb|BJ611469.1|BJ611469
EST:     TGTTAACCTGGTTGCTCTGGTCATTAATTTCAGTTCCGCTTGCATTACAG                         GTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGG
genomic: TGTTAACCTGGTTGCTCTGGTCATTAATTTCAGTTCCGCTTGCATTACAGgtaaattttc ... tttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGG
EST: gi|162174302|gb|FC350685.1|FC350685
EST:     TGTTAACCTGGTTGCTCTGGTCATTAATTTCAGTTCCGCTTGCATTACAG                         GTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGG
genomic: TGTTAACCTGGTTGCTCTGGTCATTAATTTCAGTTCCGCTTGCATTACAGgtaaattttc ... tttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGG
EST: gi|162178343|gb|FC355165.1|FC355165
EST:     TGTTAACCTGGTTGCTCTGGTCATTAATTTCAGTTCCGCTTGCATTACAG                         GTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGG
genomic: TGTTAACCTGGTTGCTCTGGTCATTAATTTCAGTTCCGCTTGCATTACAGgtaaattttc ... tttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGG

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: 22 (upstream exon), 29 (downstream exon)
Score: 3

GGTCGTTCTGTGTATACAAACATTCAAAAGTTTGTACAGTTCCAGCTTACTGTTAACCTGGTTGCTCTGGTCATTAATTTCAGTTCCGCTTGCATTACAGgtaaattttc ... tttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcccagtgatttttcattgtgatcttacatacttgtacgacgttttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCT
                       atcttac  putative branch site (score: 3)
                                            ttttgtccc  putative PPT
          atttttcatt  TA-rich tract