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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggttcttgcagaaaatgtagttacctttcatgaagcatagcacacaattttccctaaatgttgatattatctgtacatttttcag

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118316_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 5'ss of exon 5
CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGA---TGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggttcttgcagaaaatgtagttacctttcat--gaagcatagcac-acaattttccctaaatgttgatattatctgtacatttttcag
||||||||||| |||||||||||||||||||||||   ||||||||||||||| | ||||||||||||| | | |||||| ||||| |   || || |     ||| |  |||  ||||||  ||   | |  |  ||| | ||   | || | || ||||   ||| | | | ||||
CTCGCAAAGAAATTCCATCCTGATACTAATAAAGAAGATGCTGATGCAGAAAAGAAATTTCAAGAAGTTCAGCATGCCTACGAGgtatagagtcctggttatgaatat--ttatttttcatttgattaacaataggacattcttattttaaaggtgctattcgttgtgcttatctcag

upper sequence: GRMZM2G118316_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0064g01360.t01 (Vitis vinifera), 5'ss of exon 5
CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCT---GATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggttcttgcagaaaatgtag-ttacctttcatgaagcatagcacacaattttccctaaatgttgatattatctgtacatttttcag
|| ||||||||||||||||||||||| |||||||| | |   ||||| || ||||  |||||||| ||| |    || ||||||||   | ||   |  |  | |  ||| ||| | |  || | |  ||| || |||  |   ||  |      | || | | |     | |   
CTTGCAAAGAAGTTCCATCCTGATACCAATAAAGAGGATCCAGATGCCGAGAAAAAGTTTCAAGAGGTTCAAAAGGCATATGAGgt---aagtctctataacagaaatagcttatcctctattatg-gtagtacgcaaaatgtacttgaaaacctttttgtatttttggctgtag-
















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|76922542|gb|DV169052.1|DV169052
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|74237423|gb|DT645337.1|DT645337
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGC-GTGAAATATATGATCAG
EST: gi|149101262|gb|EE187374.2|EE187374
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|78088193|gb|DV516586.1|DV516586
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|93017256|gb|EB642776.1|EB642776
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|211523404|gb|FL361945.1|FL361945
EST:     AAGATGATGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATSAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|71757145|gb|DR955082.1|DR955082
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|211149678|gb|FL347659.1|FL347659
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTA-CCGTGCCTATGAA                         GTTTTGAAAGACAAATGACA-GCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAA-TGACAAGCGTGAAATATATGATCAG
EST: gi|71771526|gb|DR969463.1|DR969463
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|71427931|gb|DR808981.1|DR808981
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|91049687|gb|EB160105.1|EB160105
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|34391167|gb|CF384395.1|CF384395
EST:     AAGATGATGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|211533908|gb|FL308317.1|FL308317
EST:     AAGATGATGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|91049823|gb|EB160241.1|EB160241
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
EST: gi|71769072|gb|DR967009.1|DR967009
EST:     AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAG                         GTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG
genomic: AAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG

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), 39 (downstream exon)
Score: 127

CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 109

CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 78

CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG


Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 205

CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggtt ... catttttcagGTTTTGAAGGACAATGACAAGCGTGAAATATATGATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCGCAAAGAAGTTCCATCCTGATACTAATAAAGATGCTGATGCAGAAAAAACATTTCAAGAAGTTAACCGTGCCTATGAGgtgtgaggttcttgcagaaaatgtagttacctttcatgaagcatagcacacaattttccctaaatgttgatattatctgtacatttttcag

- - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT