Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGATTGGCTACCAAGGTGGAGAAATCCCGGAAGCAGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgacttggttgtgagtagtagttggaatttgattattgcgcattttgtcatttgttttgatctatgatgttctatgctgttacaggcagttattaataggataccacattacttagtactactacttatttactaattcttatattctcctacag

Basic information

species Physcomitrella patens
transcript PP1S37_112V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_112V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G091383_T01 (Zea mays), 5'ss of exon 3
AATGGATTGGCTACCAAGGTGGAGAAATCCCGGAAGCAGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtg-acttggttgtgagtagtagttggaatttg-attattgcgcattttgtcatttgttttgatct-atgatgttctatgctgttacaggcagttattaataggataccacattacttagtactactacttatttactaattcttatattctcctacag
|| ||  | ||||||||||||||||| || || |||||||| |||||| | |||||| |  | ||||||||| | || |||||||||||| | | |||||  |     |    ||||    |   |||| ||||||||| |     |||   ||| | ||  ||||   ||  |||         |  ||| |  |||     ||  |  ||   ||| || ||||  |  ||    |  | |  | |||
AACGGTCTTGCTACCAAGGTGGAGAAGTCGCGCAAGCAGATGAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGCGGTGTGAAGAAGgtatgcgcacttgcattcatctgactgttgtgtctaatattactgcgcatttggaa---tgtggggatttcattgtgtttc-tgtggtt--------ctgataaaaaaatagttattttttgcgtgtaactgctaatttttttgttggattggttt--tgcag
















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|18368342|gb|BJ200427.1|BJ200427
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|37849875|gb|BJ607883.1|BJ607883
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67721774|gb|BJ972033.1|BJ972033
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67709358|gb|BJ965174.1|BJ965174
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67718399|gb|BJ968658.1|BJ968658
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67723513|gb|BJ973772.1|BJ973772
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|162249820|gb|FC427597.1|FC427597
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCCCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67709437|gb|BJ965253.1|BJ965253
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67722459|gb|BJ972718.1|BJ972718
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67723434|gb|BJ973693.1|BJ973693
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67727511|gb|BJ977770.1|BJ977770
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67691760|gb|BJ951993.1|BJ951993
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|162211671|gb|FC387959.1|FC387959
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|162249821|gb|FC427598.1|FC427598
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67728039|gb|BJ978298.1|BJ978298
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|162202366|gb|FC379179.1|FC379179
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCNAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|162269513|gb|FC445069.1|FC445069
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|208345424|gb|DC912999.1|DC912999
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67719775|gb|BJ970034.1|BJ970034
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|162269512|gb|FC445068.1|FC445068
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67719209|gb|BJ969468.1|BJ969468
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|18346009|gb|BJ178052.1|BJ178052
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCA
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCA
EST: gi|37825126|gb|BJ583192.1|BJ583192
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67724705|gb|BJ974964.1|BJ974964
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67716187|gb|BJ966447.1|BJ966447
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|37824188|gb|BJ582254.1|BJ582254
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|67574155|gb|BJ946979.1|BJ946979
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
EST: gi|208355156|gb|DC926765.1|DC926765
EST:     AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAG                         ACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT
genomic: AGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCT

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), 35 (downstream exon)
Score: 171

AATGGATTGGCTACCAAGGTGGAGAAATCCCGGAAGCAGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgact ... tctcctacagACGAAGGCCGCCGGTGACGCCAAGAAGAAAAAGTAGATCTGAGATTTTTCTTCAGATTGTATAGCCGTAAAGTATACTTCTCCTGGTGGATTTACTATGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGATTGGCTACCAAGGTGGAGAAATCCCGGAAGCAGATTAAGGAGCGCAAGAACCGTTCCAAGAAGATCAGGGGCGTGAAGAAGgtacgtgacttggttgtgagtagtagttggaatttgattattgcgcattttgtcatttgttttgatctatgatgttctatgctgttacaggcagttattaataggataccacattacttagtactactacttatttactaattcttatattctcctacag

- - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG