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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctctcatttttcctgctccatgaccatgattatttatatttattgatctctacttgccatgacatttttgttttttgcttcataatacttgttaacag

Basic information

species Zea mays
transcript GRMZM2G124353_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124353_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g07570.3 (Oryza sativa), 5'ss of exon 5
AGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctctcatttttcctgctccatgaccatgattatttatatttattgatctctacttgccatgacatttttgttttttgcttcataatacttgttaacag-
||||| |||||| |||||||||||||||| || ||||| || || ||||||||||| ||||||||| | || |||| |  | |||||||||| ||||  |||||  || || |||  |  |      |  |||||||     ||  |||||  | | ||||    | | | | ||     ||||| || | || ||||| | |   
AGAGGGAGGGGATTGATGCTTGGGGTGGAGCTTGTTACCGATAGGAAGGAGAAGACACCTGCCAAGGCCGAGACCAATTTATTGTTTGAGAAACTCAAGGgtgctttc-cttattccttttctctttt--ccatgatcgc--atcattattagtttatactaataaagccctgttaacactttgcctcttcatccttgtaatccag

upper sequence: GRMZM2G124353_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 5'ss of exon 7
AGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctctcatttttcctgctccatgaccatgattatttatatttattgatctctacttgccatgacatt-tttgttttttgcttcataatacttgttaacag
||||||||||| || ||| | ||||||||||| || || |||||||| |||||||||||||||||  |||||||    |   |||||||||| ||  |||||              || |  |||||   |||||||||   | |   ||| ||    | || |||  ||| |  || ||| ||  ||  |||   | |       
AGAGGAAGGGGTCTAATGGTGGGGGTGGAACTTGTGACTGACAGAAAAGAGAAGACCCCTGCCAAAGCAGAAACTGCAGTTTTGTTTGAGAATCTTCGAGgt--------------ttgcaactcca---ccatgattaagaaaaa--attaattgtaatttaccaacacactacttatttattaatttttaactgtag-------
















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|7216798|gb|AW562920.1|AW562920
EST:     GAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|6540601|gb|AW225263.1|AW225263
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|6194732|gb|AW146836.1|AW146836
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGNNNNNNNNGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|31910695|gb|CD651553.1|CD651553
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|5123999|gb|AI745840.1|AI745840
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|60350662|gb|DN217635.1|DN217635
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|30031576|gb|CB833427.1|CB833427
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|148955021|gb|EC900524.2|EC900524
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGTTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTTTGCATGGTAACGTTTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|60338215|gb|DN205188.1|DN205188
EST:     GAAGATCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|60349531|gb|DN216504.1|DN216504
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|211311886|gb|FK975957.1|FK975957
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|60398309|gb|DN231125.1|DN231125
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|5871627|gb|AW018098.1|AW018098
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTCCTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|211061643|gb|FL451762.1|FL451762
EST:     TCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATCGTAACGTCTTCAGAA
genomic: TCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|8318607|gb|BE025352.1|BE025352
EST:     GAAGACCCCTGCCAAGACAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGAGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|44900211|gb|CK826756.1|CK826756
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         TTCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|211311888|gb|FK975959.1|FK975959
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|67014041|gb|CO442790.1|CO442790
EST:     TAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|13562273|gb|BG550493.1|BG550493
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|113701983|gb|EE679487.1|EE679487
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|78025401|gb|DV493788.1|DV493788
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|60356418|gb|DN223391.1|DN223391
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|6564029|gb|AW231651.1|AW231651
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|4776049|gb|AI665052.1|AI665052
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|148931506|gb|EC874539.2|EC874539
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|5439282|gb|AI820203.1|AI820203
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|37390746|gb|CF632607.1|CF632607
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
EST: gi|37399847|gb|CF637263.1|CF637263
EST:     GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAG                         ATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA
genomic: GAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 372

AGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAATAAAACCACCGATGTGCTTTTCGAAGGACGATGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 668

AGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAATAAAACCACCGATGTGCTTTTCGAAGGACGATGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1016

AGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAATAAAACCACCGATGTGCTTTTCGAAGGACGATGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 356

AGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctc ... ttgttaacagATCTCGGGGTACTAGTTGGAAAGGGCGGTCTGCATGGTAACGTCTTCAGAATAAAACCACCGATGTGCTTTTCGAAGGACGATGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGAAGGGGACTGATGCTTGGGGTGGAACTCGTTACGGACAGAAAGGAGAAGACCCCTGCCAAGTCAGAAACCATTGAACTGTTTGAGAAGCTCAGAGgtgccgtctctcatttttcctgctccatgaccatgattatttatatttattgatctctacttgccatgacatttttgttttttgcttcataatacttgttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA