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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTGAAAGTCGGCAGCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctttgtgttgatttcgatggttgtggagatgaggtgacgcggaattgatgtggggaaaggcggcaggtttggtttttttgtggggtttagggt...

Basic information

species Physcomitrella patens
transcript PP1S343_39V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S343_39V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os01g33050.2 (Oryza sativa), 5'ss of exon 1
AATTTGAAAGTCGGCAGCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgtt-gtttctttgtgttgatttcgatggttgtggagatgaggtgacgcggaat-tgatgtggggaaaggcggcaggtttggtttttttgtg---gggtttagggt
|    | | |  ||  |||||||| |||||||||||||||||||| || || ||||| ||||||||||| ||||| || |||||| | || ||||| |||||| |     |  |  ||  ||      ||            | | |   | | || |  |    | || ||        |   || ||||   ||||||     
AGGAAGGAGGCGGGGCGCGATGAGGTTGGAGAAGTGCTGGTTCTGCTCCTCCACCATCTACCCCGGCCACGGCATCCAGTTCGTCCGCAACGACGCCAAGgttcgcgcggtcatcctgccttttgctctttctttctcattttcatgtacagtatgttacgttttacggtggagaagcgcgcccttctgtgctcgggttt-----

upper sequence: PP1S343_39V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os07g19190.1 (Oryza sativa), 5'ss of exon 1
--AATTTGAAAGTCGGCAGCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttg----tttctttgtgttgatttcga---tggttgtggagatgaggtgacgcggaattgatgtggggaa--aggcggcaggtttggtttttttgtggggtttagggt
  | || | | | |||| |||||||| |||||||||||||||||||| || || ||| | ||||||||||| ||||| || |||||| | || ||||| ||||||     | || |  |  | ||   |    |  |  | |      |  |     |      | ||||||    |  ||        |  |||  ||| |         
GTAGTTCGGAGG-CGGC-GCGATGAGGTTGGAGAAGTGCTGGTTCTGCTCGTCCACCGTCTACCCCGGCCACGGCATCCAGTTCGTCCGGAACGACGCCAAGgttcgcgctgtcctcctcctcatcctgtgtctcttcttcgcatcctgtaggttatgtccccgtttggggatgtggatggagaagcgcgcctttccgtgcg---------

upper sequence: PP1S343_39V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA12G09090.1 (Glycine max), 5'ss of exon 2
AATTTGAAAGTCGGCA-GCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctttgtgttgatttcgatggttgtggagatgaggtgacgcggaattgatgtggggaaaggcggcaggtttggtttttttgtggggtttagggt
  || |    | |    || ||||||||||||||||| |||||||||||||| ||||||||||| || ||||| || || || ||  | ||||| || |||||    || ||   |  |   |  |  ||||     | |  |        |  ||||      ||     |    ||    ||    || |   |     
-CTTGGTCTCTTGAGGTGCAATGAGATTGGAGAAGTGTTGGTTCTGTTCTTCTACCATATACCCTGGACATGGAATCCAGTTTGTTCGTAATGATGCAAAGgtaagctcatttcttacaccactctccttgtaagtcttatctatgtgcttagggatgaaacagaactgaactaacttaaaattacattgagacctgactc

upper sequence: PP1S343_39V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA11G19410.1 (Glycine max), 5'ss of exon 2
AATTTGAAAGTCGGCA-GCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctttgtgttgatttcgatggttgtggagatgaggtgacgcggaattgatgtggggaaaggcggcaggtttggtttttttgtggggtttagggt---
  || |    | |    || ||||||||||||||||| |||||||||||||| |||| |||||| || ||||| || || || ||  | || || || |||||  | |  |    |  |      |  ||||  |  | |     | | |    ||||      ||     |    |||   | |   |  |  ||        
-CTTAGTCTCTTGAGGTGCAATGAGATTGGAGAAGTGTTGGTTCTGTTCTTCTACCACATACCCTGGACATGGAATCCAGTTTGTTCGTAACGATGCCAAGgtaatcttatctcttacaccattctccttgtaaatcttactatgctcagg---gatgaaaaagaatcaaactaacttgaaatgtgattaagacttgactcgtt

upper sequence: PP1S343_39V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA12G30680.2 (Glycine max), 5'ss of exon 2
AATTTGAAAGTCGGCAGCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgtt--------gttt-ctttgtgttgatttcg--atggttgtggagatgaggtgacgcggaattgatgtggggaaaggcggcaggtttggtttttttgtggggtttagggt
   |  |   |  |   | |||||||||||||| |||||||| || ||||| ||||||||||| || ||||| || || || ||  | ||||| || |||||         |||  ||   || | | || |  ||  |  |  |       | | |      |  | |   |||||     |  |||      || ||            
TGCTCTAGTTTGAGGCACAATGAGATTGGAGAAATGCTGGTTTTGCTCTTCAACCATATACCCTGGACATGGAATCCAGTTTGTTCGTAATGATGCAAAGgtacaaatgaagttcactccttgctaactttggaataatcttcaattcatcataaagaatttcttcttttatgaaagattaaatatttaaaaagttagtc-----------

upper sequence: PP1S343_39V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA17G05270.1 (Glycine max), 5'ss of exon 2
AATTTGAAAGTCGGCAGCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtt-tctttgtgttgatttcgatggttgtggagatgaggtgacgcgg----aattgatgtggggaaaggcggcaggtttggtttttttgtggggtttagggt
   |  |   |  |   | |||||||||||||| |||||||| || ||||| ||| |||||||||| ||||| || || || ||  | ||||| || |||||     |  ||    |  || | |      ||||       | ||        ||   || |    |     |  || ||    | |||     | |       
TGCTCTAGTTTGAGGCACAATGAGATTGGAGAAATGCTGGTTTTGCTCTTCAACCGTATACCCCGGACATGGAATCCAGTTTGTTCGTAATGATGCAAAGgtaaaaatggtttcactccttcctaactccttggaataatcttcacttcatcctaaagaatttcttcatttatgaaagattgaaatatttaaaaagatag-----

upper sequence: PP1S343_39V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA10G09780.1 (Glycine max), 5'ss of exon 2
AATTTGAAAGTCGGCAGCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgtt--------gttt-ctttgtgttgatttcg--atggttgtggagatgaggtgacgcggaattgatgtggggaaaggcggcaggtttggtttttttgtggggtttagggt
   |  |   |  |   | |||||||||||||| |||||||| || ||||| ||||||||||| || ||||| || || || ||  | ||||| || |||||         |||  ||   || | | || |  ||  |  |  |       | | |      |  | |   |||||     |  |||      || ||            
TGCTCTAGTTTGAGGCACAATGAGATTGGAGAAATGCTGGTTTTGCTCTTCAACCATATACCCTGGACATGGAATCCAGTTTGTTCGTAATGATGCAAAGgtacaaatgaagttcactccttgctaactttggaataatcttcaattcatcataaagaatttcttcttttatgaaagatcaaatatttaaaaagttagtc-----------

upper sequence: PP1S343_39V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv08s0007g03850.t01 (Vitis vinifera), 5'ss of exon 2
AATTTGAAAGTCGGCA-GCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctttgtgttgatttcgatggttgtggagatgaggtgacgcggaattgatgtggggaaaggcggcaggtttggtttttttgtggggt-ttagggt-
  |   ||  | | ||    |||||||| |||||||||||||||||||| || ||  |||| || || ||||| ||||| || ||  | ||||| || ||||| |     || | |    ||   |  || |     |  |   |      |||| |    |||         | | |  ||| ||| |  | | |||  || 
-TTACTAACCTGGACATAAAATGAGATTAGAGAAGTGCTGGTTCTGTTCCTCCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagttttctattcttttctatttttctttgtaggtcaatttc--attgctaaatggagcctttcttgctgtattttctttatttgctcttacagta

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|67569590|gb|BJ942414.1|BJ942414
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|18359891|gb|BJ191952.1|BJ191952
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|208359334|gb|DC939101.1|DC939101
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATCTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|7147860|gb|AW509782.1|AW509782
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|67692858|gb|BJ953091.1|BJ953091
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|67573936|gb|BJ946760.1|BJ946760
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|162264912|gb|FC440687.1|FC440687
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|18355620|gb|BJ187679.1|BJ187679
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|208369067|gb|DC931638.1|DC931638
EST:     CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
EST: gi|22491909|gb|BU051832.1|BU051832
EST:     CATGGCATTCAATTCGTCAGAAATGACGCTAAG                         ATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA
genomic: CATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGA

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: 31 (upstream exon), 35 (downstream exon)
Score: 18

AATTTGAAAGTCGGCAGCGATGAGATTGGAGAAGTGCTGGTTCTGTTCTTCGACCATATACCCCGGCCATGGCATTCAATTCGTCAGAAATGACGCTAAGgttgtttctt ... ttttgttcagATATTTAGGTTTTGCCGGTCGAAATGTCACAAGAATTTTAAGATGAAACGAAATCCTCGTAAGGTGAAGTGGACAAAAGCGTATAGAAAGCTTCATGGAA




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