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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacggtctgttactaaaaggagttttggcattaaaaacatgacgcacagttgtttgtcgttagttttattcacatcatgttcttctgtgtgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTG

Basic information

species Physcomitrella patens
transcript PP1S55_319V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S55_319V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os03g18510.1 (Oryza sativa), 3'ss of exon 2
caacggtctgttactaaaaggagttttggcattaaaaacatgacgcacagttgtttgtcgttagttttattcacatcatgttcttctgtgtgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTG
                      ||| | |   |       |    |      ||||   |  | ||||  | |   |   ||||   ||  || || ||| | || ||||| ||||| || |||||||| | |||  | ||||| |||||||||||| |||| ||||| |||||||||||| | |||||||| || ||||
----------------------gttcttgttatccctgtgtcttcccttagggtttactgaaactttttcttatggctaattctg--gttggttttgcagCAAGCCATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTG

upper sequence: PP1S55_319V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G083262_T02 (Zea mays), 3'ss of exon 2
caacggtctgttactaaaaggagttttggc-attaaaaacatgacgcacagttgtttgtcgttagttttattcacatcatgttcttctgtgtgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTG
                      ||| | |        ||    || |   ||  |||  |  | || ||    | |   |  |  | | ||| | || ||| | || ||||  || || || ||||| || | |||  | |||||||||||||||||| |||| || || |||||||||||  | ||||||||||| ||||
----------------------gttctagttgcccctaatgccaccctt-gtgatttaacaatggtatttgcaaaaaactaattgtatatgtat-ttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTG

upper sequence: PP1S55_319V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G058138_T01 (Zea mays), 3'ss of exon 2
caacggtctgttactaaaaggagttttggcattaaaaacatgacgcacagttgtttgtcgttagttttattcacatcatgttcttctgtgtgt-cttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTG
                      ||| | |  ||       |   |     ||||   | |  | |  ||||  ||  |  |  || | | |||  || ||| | || ||||  || || || ||||| || | |||  | |||||||||||||||||  |||| || || |||||||||||  | ||||||||||| ||||
----------------------gttctag--ttggccctgttg-gtgtccttgtgatttgacaatggtatttgcaaaaactaattgtatctgtatttgcagCAAGCTATGAAGAAAGCTGAAGCTGCGGGCAATGATAATTGTCCTGTGAAGATTAAACTAGTTGCTCCTCCACTTTATGTTCTGACCACACAGACCCTTG

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|162237618|gb|FC413051.1|FC413051
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162236800|gb|FC413479.1|FC413479
EST:     CTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162189159|gb|FC365979.1|FC365979
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162217507|gb|FC393183.1|FC393183
EST:     CGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162236799|gb|FC413478.1|FC413478
EST:     CTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162223922|gb|FC398928.1|FC398928
EST:     GCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: GCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|208363800|gb|DC943257.1|DC943257
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAAGAAAGGCAGANGCTGCTGGAACTGAANAGTGTCCTGTGAA
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGA-GAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAA
EST: gi|162202525|gb|FC380040.1|FC380040
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162206580|gb|FC382949.1|FC382949
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|208351200|gb|DC921535.1|DC921535
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|208345408|gb|DC917319.1|DC917319
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|208372240|gb|DC948043.1|DC948043
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162189158|gb|FC365978.1|FC365978
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|67694015|gb|BJ954248.1|BJ954248
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162149682|gb|FC326733.1|FC326733
EST:     GATATTGAGTTGAAATGCTTTCAGTTCGATGGGCGT-CTTCACATNCA-G                         GATGCAATGAGAAAAGCAGAGGCTGCTGGAACTGAAGAGTGTCCTG
genomic: GATATTGAGTTGAAATGCTTTCAGTTCGATGG-CGTTCTTCACAT-CAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTG
EST: gi|208389139|gb|DC945715.1|DC945715
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162259954|gb|FC435257.1|FC435257
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162163621|gb|FC339531.1|FC339531
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|22491982|gb|BU051905.1|BU051905
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|208353396|gb|DC946302.1|DC946302
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162238556|gb|FC417411.1|FC417411
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTG
EST: gi|162223923|gb|FC398929.1|FC398929
EST:     GGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: GGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|208386257|gb|DC952970.1|DC952970
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|208398568|gb|DC916089.1|DC916089
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162238555|gb|FC417410.1|FC417410
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|162237619|gb|FC413052.1|FC413052
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
EST: gi|100399885|gb|BY990670.1|BY990670
EST:     GATATTGAAGT-GAAATGCTTTCAGTTCAATGGGCGT-CTTCACATCAAG                         GATGCAATGAGAAAG
genomic: GATATTGA-GTTGAAATGCTTTCAGTTCGATGG-CGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAG
EST: gi|37836440|gb|BJ594448.1|BJ594448
EST:     CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAG                         GATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG
genomic: CTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAG

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: 35 (upstream exon), 33 (downstream exon)
Score: 17

TATTATGAACATCCGTAGGAGGATGACCCCTCAGCCATTGAAGATTCGTGCTGATATTGAGTTGAAATGCTTTCAGTTCGATGGCGTTCTTCACATCAAGgtgagctagt ... tgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacagttgtttgtcgttagttttattcacatcatgttcttctgtgtgtcttacagGATGCAATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTG
               ttagttttatt  TA-rich tract