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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTATGATGCAAATTTAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattattcttaacttctgaatttgatgagtgccagctatgaaagagtgccatgttgatgatttttctttgtttatttttgtaagcacag

Basic information

species Zea mays
transcript GRMZM2G357972_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G357972_T02 (Zea mays), 5'ss of exon 5
lower sequence: 13113.m00156 (Oryza sativa), 5'ss of exon 5
ATGCTATGATGCAAATTTAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattattcttaacttctgaat--ttgatgagtgccag---ctatgaaagagtgccatgttgatgatttttctttgtttatttttgtaagcacag------------
|||||||||||| |||||||||||||| || ||||||  ||||||||| |||||||| ||||||||||||| || |  ||| || || ||   |  |||  |   ||   |    ||||||  |    | ||  || | | | | | ||| | | ||   |               
ATGCTATGATGCGAATTTAGTTGAGATACCTGTTGAAGTGGAGACGCCTGATCATCATTATTATCATgtaagttctctttagctactaaaaagtatatgcttttaaggctcctcaaaagagcacatcatagactatatatatatatatatatatatatatattttgggtgacacag
















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|78544370|gb|DV621868.1|DV621868
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|78125802|gb|DV544186.1|DV544186
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|76926465|gb|DV170878.1|DV170878
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|24767854|gb|CA402990.1|CA402990
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|5296185|gb|AI782865.1|AI782865
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|32931110|gb|CF035922.1|CF035922
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTAGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|32796222|gb|CD948458.1|CD948458
EST:     GATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTAGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: GATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|22541936|gb|BU092374.1|BU092374
EST:     AGTTGAGATCCCCGTTGAAAAGGAGACGCCACGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCCAGAAGGTGGAAGCCTTTGAGGAGCTCACACTG
genomic: AGTTGAGATCCCCGTTGAAAAGGAGACGCCA-GATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACA-TG
EST: gi|5915516|gb|AW053157.1|AW053157
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATGATCAT                         TTTGCATTTTTCNCAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|50338839|gb|CO533965.1|CO533965
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|166574349|gb|EG160666.1|EG160666
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAG
EST: gi|12968346|gb|BG265292.1|BG265292
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|76926464|gb|DV170877.1|DV170877
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
EST: gi|78091874|gb|DV520248.1|DV520248
EST:     TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCAT                         TTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG
genomic: TAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG

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: 47 (upstream exon), 49 (downstream exon)
Score: 312

ATGCTATGATGCAAATTTAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 72

ATGCTATGATGCAAATTTAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 95

ATGCTATGATGCAAATTTAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 132

ATGCTATGATGCAAATTTAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattatt ... gtaagcacagTTTGCATTTTTCACAACCAAGAAGGTGGAAGCATTTGAGGAGCTCACATGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTATGATGCAAATTTAGTTGAGATCCCCGTTGAAAAGGAGACGCCAGATCATCACTATTATCATgtaaattattcttaacttctgaatttgatgagtgccagctatgaaagagtgccatgttgatgatttttctttgtttatttttgtaagcacag

- - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - AGATCA