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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagatacaatatacactcttccttaatatactgttacttctcgagtgtttcaaatattcaatgtcctagaaggtttgctcaactaaatttacttctttctgataccag

Basic information

species Zea mays
transcript GRMZM2G104294_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 16
GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagatacaatatacactct---tccttaatatactgt--tacttctcgagtgtttcaaatattcaatgtcctagaaggtttgctcaactaaatttacttcttt-ctgataccag
|||||  ||| || ||||||| || ||||||||||| |||||||| |||||||| ||||| ||| | |||||||| |||||||||||||||   |||||||| || | | ||| || |||    |   ||    ||| |  | ||| ||  |   ||| | ||   ||| |||    |  |  |||  ||| |||    || | | |||||| |||
GCAAAACTTCATTCAGGAGGGTGCACTTTCTGAGCTGATTGTTGCCTTCTCTCGTGAAGGACCAGCCAAAGAATACGTGCAGCATAAGATGACAGAGAAGgttagtt-cgatacacgctccacatttctaccgcactatgctgcttttcttgaacttcta-tacagaatttccccacacatg-gctatactcaatgaggttttctgctgatatcag
















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|211061849|gb|FL232858.1|FL232858
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|32928790|gb|CF033602.1|CF033602
EST:     CTCGGGAAGGGCCAGCGAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|113701122|gb|EE678626.1|EE678626
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|37374425|gb|CF623569.1|CF623569
EST:     GGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: GGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|60353207|gb|DN220180.1|DN220180
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|60398924|gb|DN231740.1|DN231740
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|60340539|gb|DN207512.1|DN207512
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|60344210|gb|DN211183.1|DN211183
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|211021947|gb|FL480535.1|FL480535
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATTAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|60398791|gb|DN231607.1|DN231607
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|32835489|gb|CD975167.1|CD975167
EST:     CTCGGGAAGGGCCAGCGAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|74239509|gb|DT647423.1|DT647423
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|32929541|gb|CF034353.1|CF034353
EST:     CTCGGGAAGGGCCAGCGAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|32835138|gb|CD974816.1|CD974816
EST:     CTCGGGAAGGGCCAGCGAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|211061847|gb|FL232856.1|FL232856
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|61119293|gb|DN560254.1|DN560254
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|60399770|gb|DN232580.1|DN232580
EST:     CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|32921780|gb|CF026592.1|CF026592
EST:     CTCGGGAAGGGCCAACTAAAGAAT--GTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
EST: gi|32920698|gb|CF025510.1|CF025510
EST:     CTCGGGAAGGGCCAACTAAAGAAT--GTGCAGCATAAGATGGTGGAGAAG                         GCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC
genomic: CTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGC

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 229

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 408

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 434

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 440

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagataca ... ctgataccagGCCACAGAAATTTGGAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATGTGCAGCATAAGATGGTGGAGAAGgtcagatacaatatacactcttccttaatatactgttacttctcgagtgtttcaaatattcaatgtcctagaaggtttgctcaactaaatttacttctttctgataccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA