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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTATGGATCACTGCTATGTTTCAGGAACGGTTGGTGATGACAGCTGGTACAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcctatgcataatataggtctgatatactctttagatgttacttggtatcaaaacaaaaatggaataatgattggtaatgctatttattctagatctattttatttgggtcactgatggatatcatgtaatacaacag

Basic information

species Zea mays
transcript GRMZM2G043862_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043862_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g57210.1 (Oryza sativa), 5'ss of exon 10
TGTATGGATCACTGCTATGTTTCAGGAACGGTTGGTGATGACAGCTGGTACAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtac-ttttcctatgcataatataggtctgatatactctttagatgttacttggtatcaaaacaaaaatggaataatgattggtaatgctatttattcta-gatctattttatttgggtcactgatggatatcatgtaatacaacag
|||||||||||||||||   ||||| |  | | |||||||||| |||||||||||| ||  ||||| | ||||| || || ||||| ||||||||| ||||||   |  | | ||| |  | ||  |||||    || | |      || ||| ||| |||| |||  ||||| | ||||  | || | | | |||  |  ||   || | || |  ||   | |  |                   
TGTATGGATCACTGCTACAATTCAGAAGTGTTCGGTGATGACAACTGGTACAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctaccttgtgcctttt-taattctga----ctatatcagaaataattgatatgaaaataaac-tggaaaactgat--gcaa-gttttctatcttgtgaatgatgtcatctctgtacattacag-------------------
















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|60394527|gb|DN227397.1|DN227397
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|26457476|gb|CA829059.1|CA829059
EST:     CAAGACGGTCATTTTAGCTGG-GGTTCGTCG-GCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|211216600|gb|FL362617.1|FL362617
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|78180885|gb|DV551258.1|DV551258
EST:     ACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: ACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|7844623|gb|AW787845.1|AW787845
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|211049730|gb|FL339082.1|FL339082
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|149100035|gb|EE186087.2|EE186087
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCCCCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|113701275|gb|EE678779.1|EE678779
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|78544483|gb|DV621981.1|DV621981
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|6918321|gb|AW399851.1|AW399851
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|40303469|gb|CK347856.1|CK347856
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|110532724|gb|EE036904.1|EE036904
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTTCCAG                         AGAGGCTGGAGAAAGAGCTTCACCAACTTTTTCCTCCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
EST: gi|110515665|gb|EE020253.1|EE020253
EST:     CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAG                         AGAGGCTGGGGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG
genomic: CAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAG

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), 47 (downstream exon)
Score: 46

TGTATGGATCACTGCTATGTTTCAGGAACGGTTGGTGATGACAGCTGGTACAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

TGTATGGATCACTGCTATGTTTCAGGAACGGTTGGTGATGACAGCTGGTACAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

TGTATGGATCACTGCTATGTTTCAGGAACGGTTGGTGATGACAGCTGGTACAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 71

TGTATGGATCACTGCTATGTTTCAGGAACGGTTGGTGATGACAGCTGGTACAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcc ... aatacaacagAGAGGCTGGAGAAAGAGCTTCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTATGGATCACTGCTATGTTTCAGGAACGGTTGGTGATGACAGCTGGTACAAGACGGTCATTTTAGCTGGTGGTTCGTCGTGCTTGCCTGGTTTACCAGgtacttttcctatgcataatataggtctgatatactctttagatgttacttggtatcaaaacaaaaatggaataatgattggtaatgctatttattctagatctattttatttgggtcactgatggatatcatgtaatacaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG