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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA

Basic information

species Physcomitrella patens
transcript PP1S218_19V6.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 15
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctg-catatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                                                                  |  ||| |||    ||  |   |    |||  | ||   | ||  | ||  |  | || |||| ||   |     || || ||    || |||||||||||| |||||| |   ||| ||  |  |||||||||||||||| ||||||||||| |||||| |||| || || || || || || || |||  
----------------------------------------------------------------gtaaagtcatttaccctcagtttcacgccttac-tgaatgatctgacagtggagataaattgtct-caaattagcaatcatcttatgtatgaagGTGATATCGGTGAGTGGCAACCAGACGGCACAATGAAGATCATCGACAGAAAGAAGAACATTTTCAAGCTGTCCCAAGGGGAGTATGTAGCAGTGGAGGT

upper sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: LOC_Os06g06350.2 (Oryza sativa), 3'ss of exon 10
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggt--ctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                                                | ||| ||||  | |         | | ||   | |   | |||  |||| |  || | |     |  | || ||| |  ||| || |  | |  | | ||| || | |||| ||| | || |||||| |   | |||| |||||||| ||||| ||||||||||| || || |||||| | |||||||| ||||| ||||| || || ||
----------------------------------------------gttagctgtttctataa---------tctctgggacatgctagttgactataatggcattat----ttttttcagatgatgactatatgccaaataccat-gtataa-tacagGGGATGTTGGCGAGTGGCAACCAAATGGGTCCTTGAAAATCATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAA

upper sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 15
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                                | ||| |||    |   |  ||| || ||         ||||||  |||      || ||   |   | |  | ||| | | ||||         |  |   || |  ||  | ||    |||||||||||||||||||||| |     ||||  |  |||||||||||||||| |||||||||||||||||| |||| ||||| || || || || || |||  
-------------------------------gtgaaagaataaaaaaaatcatttctcact---------tcttttaatttgcacctaactga--aggatcagtcagtgaagcagctggtcgattcgtggaacttg-tcatcaccctatgtgtgcagGTGATATCGGGGAGTGGCAATCCAATGGCACGATGAAGATCATCGACAGAAAGAAGAACATCTTCAAGCTGTCCCAGGGGGAGTATGTGGCAGTTGAGGT

upper sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                                                     | ||     |||   ||  ||    |  | |  ||| ||  | |   |           ||   |  | |   || |    |  |  | ||      |||||||| || || || |||||| ||   || |||  | |||||||||| ||| | |||||||||||||||||| | |||||||| || |||||||| || |||||
----------------------------------------------------gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatattt-----actgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

upper sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: AT1G49430.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                                                   || |    || ||    | | ||     || | | |  ||  ||| |  | ||   ||    |  || |||  ||  | ||| |||||   ||  ||  |  | ||| ||||| || || ||| |  ||||||||||  ||||||||||||| |||||||||||||||||||||||||| || |||||||| |||||||| || ||
------------------------------------------------agactctaaaacttagtctatattttaaccattagattg--ttagttacaaaagcaacttg----tattggataatgttgaaatt-tgatttcatttatatga--gtagGAGATATTGGAGAATGGCAAGAAGATGGATCAATGAAGATCATCGATAGGAAGAAGAACATCTTCAAGTTGTCTCAAGGTGAATATGTTGCTGTTGAAAA

upper sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EDO96800 (Chlamydomonas reinhardtii), 3'ss of exon 12
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                       |||||| ||     |  | |  | |   |     | | || | |    |         ||   | |  |     |   ||||     |||   | || |      | |  | ||     |     | ||    || ||  | || |||  |  ||  || ||| || | |||||||||||| | |||||||||||||||||| |    ||                        
----------------------tgttttcctt----gtgctctttaacacacacacacacacacacacacacacacacacacgcacgcac-gcacgcacgcacacaaacaaacacgtacacaca---cagACGCGGACGGCTTCTTCCACAC---GGGCGACGTGGGCGAGCTGGTGACGGACGGAACCCTCAAGATCATCGACCGCAAGAAGAACATCTTCAAGCTCAGCCA------------------------

upper sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ23443 (Selaginella moellendorffii), 3'ss of exon 15
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                                                                                                ||   || |    |||       |  ||||    |  ||||      |  |     |  ||| |||||||| ||||||     | | ||| ||||||| ||||| ||||||||||||||||| |||||  | || || || |||||||| ||||| |||||
-----------------------------------------------------------------------------------------------gtagggactcaaaagaaacttgctacgtggttctta--ctgaacgaggtttt-----tatagGAGATATCGGAGAGTGGCTACCAAACGGAGCCTTGAAAATCATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAA

upper sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ25426 (Selaginella moellendorffii), 3'ss of exon 15
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                                                                                                ||   || |    |||       |  ||||    |  ||||      |  |     | |||| |||||||| ||||||     | | ||| ||||||| ||||| ||||||||||||||||| |||||  | || || || |||||||| ||||| |||||
-----------------------------------------------------------------------------------------------gtagggactcaaaagaaacttgctacgtggttcgta--ctgaacgaggtttt-----tacagGAGATATCGGAGAGTGGCTACCAAACGGAGCCTTGAAAATCATAGACAGGAAGAAGAACATTTTCAAACTCTCGCAAGGCGAATACGTCGCTGTAGAGAA

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|162209089|gb|FC385113.1|FC385113
EST:     GTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: GTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
EST: gi|162162560|gb|FC338654.1|FC338654
EST:     GATGGCTGGTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: GATGGCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
EST: gi|18335322|gb|BJ167340.1|BJ167340
EST:     GCGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: GCGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
EST: gi|162167701|gb|FC344015.1|FC344015
EST:     GCGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: GCGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
EST: gi|162199026|gb|FC372377.1|FC372377
EST:     GCGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: GCGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
EST: gi|162171310|gb|FC347235.1|FC347235
EST:     CGGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: C-GGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
EST: gi|162209090|gb|FC385114.1|FC385114
EST:     CTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: CTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
EST: gi|162170150|gb|FC347062.1|FC347062
EST:     GCTGGTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: GCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
EST: gi|162199212|gb|FC375048.1|FC375048
EST:     CGGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCG                         GTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA
genomic: C-GGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGA

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: 24 (upstream exon), 13 (downstream exon)
Score: 2

AGGGGTGAAATTTGCATTAGGGGTAGTACTTTGTTCTCCGGTTACTACAAGCGGCAAGATCTCACTGATGAGGTTCTCGTCGATGGCTGGTTCTCCACCGgtaatgtctt ... aaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
                             ttctgat  putative branch site (score: 2)
                                            taaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggtctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC