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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgtatagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaacatatctctttgcagtcaagcttttactgcac...

Basic information

species Zea mays
transcript GRMZM2G135283_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g52840.3 (Oryza sativa), 5'ss of exon 2
GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgtatagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaac--atatctctttgcagtcaagcttttactgcac
 |  ||||||||||| ||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||||||||||||||| || | |  | |||   | |      | | |||||   || |    |    ||||  || | |   ||| |  || |   ||     ||| ||||  
ATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaa-tcattttcactctt-tatcttgccttgtcatgtttttatatgaactccagctttcatgcgcatcaatagcctttagtcctcttttgtttcctgctt

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 5
-----------------------GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgtatagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaac--atatctctttgcagtcaagcttttactgcac
                        |  ||||||||||| ||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||||||||||||||| || | |  | |||   | |      | | |||||   || |    |    ||||  || | |   ||| |  || |   ||     ||| ||||  
CTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaa-tcattttcactctt-tatcttgccttgtcatgtttttatatgaactccagctttcatgcgcatcaatagcctttagtcctcttttgtttcctgctt

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 5
GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgtatagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaacatatctctttgcagtcaagcttttactgcac--------
|| |||||| ||||||||  |  | ||||| |||||||| ||||| || || || ||||| ||||| ||||||||||||||||     |||  | |      ||| |   |||     | |     | |   |||| | ||  |  |||  |  | |  |    |   | |    ||        
GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaagaatatcattt-----taattttggttaga---ctaaacttttttccccttgtatgcaagtatacatggtagttgatttgtcctaagcatacaagtatac

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 5
GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgtatagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaacatatctctttgcagtcaagcttttactgcac-------
|| |||||| |||||||||||||| |||||||| ||||| || || |||||||  |||||||| || |||||||||||||||     | |  |   |   |  || | |  ||  ||||  | |  | | |   ||   ||   |  | |       || |     || ||||||||       
GTATATTGACATGGCAGAGTCCTTATGTCAGAAGCGTGCATTAGAAGCTTTCCAGTTGGACCCTGCAAAATGGGGAGgtaaa----cgaaccgggcatttg--atttatcctagcttgctttcttttctttcagttagctgatgatgtttactgcaacaattgca-ttatactgcacttcagtt

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 5'ss of exon 5
GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgt-atagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaacatatctctttgcagtcaagct-tttactgcac
||  || || |||||||| |||||||| ||||| ||||||||||| || || || ||||| || || |||||||||||||||  | | | ||  | || |  ||| ||  ||    |   |||||   |      | |||| ||||  | | |  |  |  | ||    ||||  |   
GTACATGGACATGGCAGAATCCTTGTGCCAGAAGCGTGCTTTGGAAGCATTTCGGTTGGATCCTGCAAAATGGGGAGgtaaatacatatgatcatgta-cgtcaagatagatgccatctgcatgtttcaaagcaatgtttt-tgaaattcttttctcaccatgaactggtttaaagttt

upper sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 5
GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgt-atagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaacatatctctttgcagtcaagct-tttactgcac
||  ||||| |||||||| |||||||| ||||| ||||||||||| || || || ||||| || || |||||||||||||||  | | | ||  | ||    ||| ||  ||    |   |||||   |      | |||| ||||  | | |  |  |  | ||    ||||  |   
GTACATTGACATGGCAGAATCCTTGTGCCAGAAGCGTGCTTTGGAAGCATTTCGGTTGGATCCTGCAAAATGGGGAGgtaaatacatatgatcatgta-tgtcaagatagatgccatctacatgtttcaaagcaatgtttt-tgaaattcttttctcaccatgaactggtttaaagttt

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|211286152|gb|FL173733.1|FL173733
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|211286141|gb|FL173722.1|FL173722
EST:     CAGAAACGTGCTTTGGAGGGCTT-CCGTTTGGACCGGGCGAAATGGGGAG                         TGAATGTGCACCCTCTATCCGGNTCGCCCGCCA-CTTCCATGGATACACTG
genomic: CAGAAACGTGCTTTGGAGG-CTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|21987802|gb|BQ779330.1|BQ779330
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|211284346|gb|FL173719.1|FL173719
EST:     TCAGAAACGTGCTTTCGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|149078907|gb|EE167727.2|EE167727
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|211349901|gb|FL349172.1|FL349172
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|211379738|gb|FL173738.1|FL173738
EST:     AGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGATAATGGGGGAG                         TGAATGTGCAACCTCTATCCGG
genomic: AGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGA-AATGGGG-AGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGG
EST: gi|148973319|gb|EE024404.2|EE024404
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|149012532|gb|EE042603.2|EE042603
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|148946029|gb|EC891328.2|EC891328
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|149048905|gb|EE048404.2|EE048404
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|148958252|gb|EC904466.2|EC904466
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|211286148|gb|FL173729.1|FL173729
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|60351519|gb|DN218492.1|DN218492
EST:     GGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: GGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|71299012|gb|DR785498.1|DR785498
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|148930308|gb|EE284699.2|EE284699
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|60346600|gb|DN213573.1|DN213573
EST:     TTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|148969981|gb|EE020895.2|EE020895
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|211284347|gb|FL173720.1|FL173720
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|149081312|gb|EE170425.2|EE170425
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|211379744|gb|FL173744.1|FL173744
EST:     TCAGAAACGTGCTTTCGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGGTCGCCCGCCAA
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAA
EST: gi|148947246|gb|EC892606.2|EC892606
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|149089957|gb|EE179246.2|EE179246
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
EST: gi|148945831|gb|EC891120.2|EC891120
EST:     TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG
genomic: TCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatctt ... acctttatagTGAATGTGCAACCTCTATCCGGTTCGCCCGCCAACTTCCATGTATACACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgtatagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaacatatctctttgcagtcaagcttttactgcac

- - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - -  TGGAGG