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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaatgtcatatgttggggtacccgtttatttcacagtattctcaccagaaattggtataagcatattgttgaaatgcgctaattgagctttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG

Basic information

species Zea mays
transcript GRMZM2G038401_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 7
----------tccaatgtcatatgttggggtacccgtttatttcacagtattctcaccagaaattggtataagcatattgttgaaatgcgctaattgagctttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG
          ||||   |   ||| |   |    |   |  |||||| | ||  ||   |||  || ||    | || |||  | |||   | ||||  | ||||| |||||||||||||| |  ||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| || || || ||||| || |||||||
atttgttcattccatatttccatgattacgctgtcaaatcgttcacaatgttggcagtggaa--tgata----cctaatgt--agatGTTTTGATTG--CCTTGTTACAGGTTTTGATTGGAAGGATCTCCACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACCTATGCGCAGGTTGCTGTATACGGTTTCAGCGAAAAGG

upper sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 7
----tccaatgtcatatgttggggtacccgtttatttcacagtattctcaccagaaattggtataagcatattgttgaaatgcgctaattgagctttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG
    |    |   ||||        |   |   |      ||| || |          || |     | |  || ||| | | | | |||     | | | |||||||||||||| | ||| || || || || || ||||| |||||||| || || || ||||||||||| |||||||| || |||||||||||||| ||||
atatttgcttacaatattagaaaagaaaagacgaacctctagtgttttgtttcag---tgtttccgccgtgatgatgacagg-gttcatttcctatggatgcagGTTTTGATTGGTAGAATATCGACAGGAGCCCAAAATGATCTGGAGAAGGTAACAAAGATGACATATGCTCAGGTCGCAGTCTATGGTTTTAGTGACAAGG

upper sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv08s0007g00550.t01 (Vitis vinifera), 3'ss of exon 1
--tccaatgtcatat--gttggggtacccgtttatttcacagtattctcaccagaaattggtataagcatattgttgaaatgcgctaattgagctttgttt-cagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG
  |   |||| || |  |       | | |||      |||| |     |  ||||  |    ||| |   |||      ||  | |||  |  | ||     |||| ||  | || || ||||||||||| || ||||||||| |||||||||| || || ||||  ||||| || || || || |||||||| ||||| ||||
cttttgatgtgattttggacaaataatctgttatgaaaacagaaaagcaattagaatctatcgtaatccatttg-----gtgttcaaatgaaaatctggaagtagGTATTATTGGGGAAGATCTCAACTGGAGCCCAGAATGACTTGGAGAAAGTGACAAAGATGATCTATGCCCAAGTAGCAGTCTATGGTTTCAGTGAGAAGG

upper sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------------------------tccaat-gtcatatgttggggtacccgtttatttcacagtattc----tcaccaga-aattggtataagcatattgttgaaatgc--gctaattgagctttgttt----cagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG
                                                                                      |  | | |  ||||  | |    |  |   |  |   ||| ||     ||   ||| ||   || | ||  || ||||||  |     ||  | |  | ||| ||    |||||  || | || ||||| ||||| ||||| ||||||||| ||||||||||||| |||||||| |||||||| || || || ||||| ||||||||||| |
gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagt-taatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAG

upper sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S39_149V6.1 (Physcomitrella patens), 3'ss of exon 7
tccaatgtcatatgttggggtacccgttta--tttcacagtattctcaccagaaattggtataagcatattgttgaaatgcgcta-attgagctttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG
  ||  || |  | ||   |||   ||  |  |||  | ||| ||  |      |  || | ||   |  || |   | ||  |  ||    | ||    ||||| ||| | |||||||| ||||| || ||||| ||||||||||||||||| || |||||||||||||| || ||||| || ||||| || |||||||| |
cacatcgttacttcttaatgtaagagtcaaggtttatcggtagtcgtagatttgaccgg-acaat--tgctgattctaagcattgtatccttcattcacgcagGTATTGTTAGGCAAAATTTCAACAGGAGCTCAAAATGACCTGGAGAAAGTAACGAAAATGACATATGCTCAAGTCGCGGTTTATGGGTTCAGTGAAAAAG

upper sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S456_6V6.1 (Physcomitrella patens), 3'ss of exon 8
tccaatgtcatatgttggggtacccgtttatttcacagtattc--tcaccagaaat-tggtataagcatattgttgaaatgcgctaattgagct--ttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG
   ||    | |   ||     ||  || ||| | | | ||    |      || | | || |    | |||| | |  |    || ||| | |  ||    ||||| ||||| |||||||| || || || || ||||||||  | |||||||| || ||||||||||| || || ||||| || ||||| |||||||| || |
--taaga--agagaatgaaagtcctcttcattactctggatctgattgttttaagtcttgttttttaacattgattatttat-ttatttgtgttacttcacacagGTATTGATAGGCAAAATATCGACAGGGGCGCAGAATGATTTAGAGAAAGTGACGAAAATGACATACGCCCAAGTCGCAGTTTATGGGTTTAGTGATAAAG

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|211346930|gb|FK977754.1|FK977754
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|60358258|gb|DN225231.1|DN225231
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|211346929|gb|FK977753.1|FK977753
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|31353784|gb|CD438141.1|CD438141
EST:     CTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGCTTTCTCAGAATGACCTGGAGAAAGT
genomic: CTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTG-GTGCTCAGAATGACCTGGAGAAAGT
EST: gi|32928350|gb|CF033162.1|CF033162
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|71332347|gb|DR803114.1|DR803114
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|60343952|gb|DN210925.1|DN210925
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|211346933|gb|FK977757.1|FK977757
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|61118761|gb|DN559722.1|DN559722
EST:     AGCTTTTTGATATGACATACATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|60355707|gb|DN222680.1|DN222680
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGNAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|32934811|gb|CF039623.1|CF039623
EST:     AGCTTTTTGATATGGCATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGGATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|211346936|gb|FK977760.1|FK977760
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|60394632|gb|DN227502.1|DN227502
EST:     AGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|67013763|gb|CO442512.1|CO442512
EST:     AGCTTTTTGATATGACATGCATGACATTANGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGNAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|94473016|gb|EB701974.1|EB701974
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|6637060|gb|AW261332.1|AW261332
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAG
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAG
EST: gi|78544110|gb|DV621608.1|DV621608
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
EST: gi|213169945|gb|FM183968.1|FM183968
EST:     AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAG                         GTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT
genomic: AGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTT

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: 177

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 262

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

AGGCTTTGCACAATACGTCCCAAATGAAAATCTTTTGATGACAAAAGAGCAGCTTTTTGATATGACATGCATGACATTAGGTGGCCGTGCTGCAGAGGAGgtacattttc ... tttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accagaaattggtataagcatattgttgaaatgcgctaattgagctttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG
                                            ctttgtttc  CT-rich tract
                   atattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaatgtcatatgttggggtacccgtttatttcacagtattctcaccagaaattggtataagcatattgttgaaatgcgctaattgagctttgtttcagGTTTTGATTGGCAAAATCTCAACTGGTGCTCAGAATGACCTGGAGAAAGTTACCAAAATGACATATGCACAGGTCGCCGTGTATGGTTTTAGTGAAAAGG

- - - - - tatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa