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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataattgattcccgtttgaatcttattcatttcaacttttaagaatactattccctcttcaaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC

Basic information

species Zea mays
transcript GRMZM2G015989_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 5
--------gataattgatt-cccgtttgaatcttattcatttcaacttttaagaatactattccctcttcaaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
        ||  ||||  | || ||||||||| || ||||     ||    | |  ||||||    ||| |||  ||||||| | |   | |  |||   |  || |||||||| ||||| || ||||||||||||||||| || ||||| ||||||||||| |||||||| || ||||||||||| |||||||| |||||||| || |
gaattcaggagcattggctgccagtttgaatcgtactcatcc--gct----acagcactatttttgcttgaaa--tttgaatctatcatattg-catgcaactttgcagGTTGAAGACAGCGAACTTGCTGATGTTGCTGCGGTAAGTGCTGGAAATAACTACGAAATTGGCAACATGATAGCTGAAGCTATGAACAAGGTTGGACGAC

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
-gataattgattcccgtttgaatcttattcatttcaacttttaagaatactattccctcttcaaaatt-ttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
  ||  |||| |    || || ||||| ||     | || ||         ||   || |  |  ||| ||||  |||| |  ||    ||    ||| |||||||| |||||||| || || |||||||| ||||||||||| ||||| || || ||| | || |||||||| || || || |||  ||| ||||| ||  
gtattgttgactta-attagattcttaatc----tagctcttt------tcatgtgctttagaggattcttgatcatgtagctctt---ttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
gataattgattcccgt--ttgaatcttattcatttcaacttttaagaatactattccctcttcaaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
  ||| | | |    |  |  ||  |  ||| | | || ||||    |  ||||  |      || ||  |  | | |||     |    |||  | || ||||||| |||||||| ||||||||||| || || ||||||||||| |||||| | ||| |||| | |||||| ||||| || ||||  || || ||  || 
-gtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctatagc------aagatggtctaaaggttatgtca----ttggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 5
gataattgattcccgtttgaatcttattcatttcaacttttaagaatactattccctcttcaaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
     || |      |   | |||  ||| ||| |  | |||||| |  | |||       ||  || ||||| |        ||    ||    |  ||||||| |||||||| ||||| |||||||| || ||||||||||| || ||| | |||||||| |||||||| ||||| || ||||  || || ||  || 
---gtttcaaatttatagaactctctttcttttaatatgttaagagtctttttcaa-----aaggttctgaatgt--------aagtcatgtcgatgtagGTTGAAGACAGTGAACTTGCAGATGTTGCAGCTGTTAGTGCGGGTAACAACGACGAAATTGGAAATATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------gataattg-attcccgtttgaatctta--ttcatttcaacttttaagaatac-tattccctctt---caaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
                                      || ||||   |  |   |  | |||||  ||||||| || |||||| | | | | ||  || ||    | ||| |  |  ||  |  ||    || || ||| ||||||||| ||||||||||| || |||||||| || |||||||| ||||| ||| ||||| | || |||||||| || || || ||||  || || || ||  
gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggat-ctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 4
gataattgattcccgtttgaatcttattcatttcaacttttaagaatactattccctcttcaaaattttgaatatgttg---gactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
   || |||||   | ||  |   |    |||  || ||||  |  |     |  |  |    | ||| |||| | ||    | |  | || | |  || |||||||| |||||||| || || ||||| |||||||||||||| ||||| ||||||||| | ||  ||||||||||||| ||||||    | |||||  |  
--gaactgattttagcttctaagctgagtattgaaaattttgcgtttgg-gctttccatgtggattttggaatgtattttttgtcataaatataactttgcagGTTGAAGACAGTGAACTAGCAGATGTGGCTGCAGTTAGTGCAGGAAACAACTATGAAGTAGGATATATGATAGCTGAAGCTATGGGTCAAGTTGGCAGAA

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|32841380|gb|CD981061.1|CD981061
EST:     GAAAACAGCCAAAGCAACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTTGAGGACAGTGAGCTTGCTGATGTTTGCTGCAGTTAGTGCGGGAAA
genomic: GAAAACAGCCAAAGCA-CTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTT-GAGGACAGTGAGCTTGCTGATGTT-GCTGCAGTTAGTGCGGGAAA
EST: gi|211453373|gb|FL117934.1|FL117934
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATNGT-GCTGCAGTTAGTGCGGGAAAATA
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGAT-GTTGCTGCAGTTAGTGCGGGAAA-TA
EST: gi|29167881|gb|CB411141.1|CB411141
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|28568974|gb|CB280849.1|CB280849
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|32840608|gb|CD980289.1|CD980289
EST:     AGAAAACAGCCAAAGCACTAGTCAGGGAACTCCAAAAGATGTCCAAGGAG                         GCTGAGGACAGGGAGCTTGCTG
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTG
EST: gi|67040018|gb|CO466273.1|CO466273
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|211451229|gb|FL117917.1|FL117917
EST:     GAAAACAGC-AAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGGAG                         GNTGAG-ACAGTGAGCTTGCTGATGGTGCTGCAGTTAGTGCGGGTAATAA
genomic: GAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGG-AGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAA
EST: gi|32840617|gb|CD980298.1|CD980298
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGCTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|211455503|gb|FL117949.1|FL117949
EST:     AGAAA-CAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GT-GAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAAATA-
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAA-TAA
EST: gi|31355200|gb|CD439557.1|CD439557
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|211453368|gb|FL117929.1|FL117929
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATTGT-GCTGCAGTTAGTGCGGGAAATAA
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGAT-GTTGCTGCAGTTAGTGCGGGAAATAA
EST: gi|67016492|gb|CO445241.1|CO445241
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|47961558|gb|CN844267.1|CN844267
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCNAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCA
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCA
EST: gi|211451956|gb|FL157392.1|FL157392
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|32840620|gb|CD980301.1|CD980301
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|32934116|gb|CF038928.1|CF038928
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|32840586|gb|CD980267.1|CD980267
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAAC
EST: gi|211453376|gb|FL117937.1|FL117937
EST:     AGAAA-CAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GT-GAGGACAGTGAGCTTGCTGATNGT-GCTGCAGTTAGTGCGGGAAATTA
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGAT-GTTGCTGCAGTTAGTGCGGGAAATAA
EST: gi|87155572|gb|DY400361.1|DY400361
EST:     AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAG                         GTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTT
genomic: AGAAAACAGCCAAAGCACTAGTCAGTGAACTCCAAAAGATGTCCAAGGAGgtaacttttg ... gatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactattccctcttcaaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
             ttcaaaattttgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataattgattcccgtttgaatcttattcatttcaacttttaagaatactattccctcttcaaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - ttcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgttg