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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGTTACGGTGAGTTTTTCGTTGCGCGCTGCTTTGTAATTGCCAGGTGTGAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattgagtgtcgtctccgggtctgatcttggggtgaagagtaggggtgaaagtacttgccttagggcgtggagttgggagcccaatcgatttcat...

Basic information

species Physcomitrella patens
transcript PP1S55_61V6.2
intron # 1
splice site 5'
intron type U2

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|67573946|gb|BJ946770.1|BJ946770
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|100424415|gb|BY958473.1|BY958473
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|208357560|gb|DC934068.1|DC934068
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|100395154|gb|BY953619.1|BY953619
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|208385281|gb|DC915081.1|DC915081
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|100447697|gb|CJ971996.1|CJ971996
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|67574099|gb|BJ946923.1|BJ946923
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|208379032|gb|DC907781.1|DC907781
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCANCAACGCGACTGCTTCAACAGGGTTCGNGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|67507485|gb|BJ940367.1|BJ940367
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|208376388|gb|DC932284.1|DC932284
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|100406376|gb|BY955596.1|BY955596
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|100388356|gb|BY951958.1|BY951958
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|100399700|gb|BY972849.1|BY972849
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
EST: gi|100389716|gb|BY952522.1|BY952522
EST:     GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACG                         AAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG
genomic: GAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCG

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: 29 (upstream exon), 31 (downstream exon)
Score: 6

AGTGTTACGGTGAGTTTTTCGTTGCGCGCTGCTTTGTAATTGCCAGGTGTGAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattg ... aaaattgcagAAGCCATGGCCTTCACCAACGCGACTGCTTCAACAGGGTTCGTGACTTCCGTGATGATTCTGTTTCTGTTGACAACCGTCTCTCCAAGCTTGGTGCAGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGTTACGGTGAGTTTTTCGTTGCGCGCTGCTTTGTAATTGCCAGGTGTGAAGGCCAGGACTGAAGGTGCGGAGTGGAGACAAGCTCAGTGCGGAAACGgtgagtattgagtgtcgtctccgggtctgatcttggggtgaagagtaggggtgaaagtacttgccttagggcgtggagttgggagcccaatcgatttcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA