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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCTCGCCGGTAGGCGGCGCAGGTGGAGCACGCTCGTGGTCTGCGCGGCCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctcttgctcttcaacttaccatcggttcatttcattttagcagcttgttctggtgggattggaggaggctataggctgcccaataaccggttta...

Basic information

species Zea mays
transcript GRMZM2G094831_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094831_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g40040.1 (Oryza sativa), 5'ss of exon 1
GGTTCTCGCCGGTAGGCGGCGCAGGTGGAGCACGCTCGTGGTCTGCGCGGCCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaat--tctcttgctcttcaacttaccatc---ggttcatttcattttagca--gcttgttctggtgggattggag--gaggctataggctgcccaataaccggttta
||| | | |  | |||||||| || |||  | |||||||||| |||||||||||||||||||||||||||||   |||||||||||||||||| |||||||||||  || |   ||   | | | ||| |    | |||  |   |||  |||  | ||||||| ||| |  | ||   |||      || ||   |||          
GGTCCCCTCGAGGAGGCGGCGAAGATGGGACGCGCTCGTGGTGTGCGCGGCCCCCGACGAGGAGAAGATTACGCGGCGGTCGCCCCTCGATTTTCCCATCgtaataatccccctcttcccgattcaccgtgaaagattctatcggtttatgcactgattgttctcgtgtgtgttgaattgagtgctcgggttgaggaatt---------
















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|60340962|gb|DN207935.1|DN207935
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|211435360|gb|FL223968.1|FL223968
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|166694311|gb|EG189298.1|EG189298
EST:     ATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: ATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|18173813|gb|BM349201.1|BM349201
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|67042012|gb|CO468267.1|CO468267
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|60353186|gb|DN220159.1|DN220159
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|211437952|gb|FL223978.1|FL223978
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|211246320|gb|FL449829.1|FL449829
EST:     CGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|71431939|gb|DR812989.1|DR812989
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|89762068|gb|DY689834.1|DY689834
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|211437943|gb|FL223969.1|FL223969
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|211435358|gb|FL223966.1|FL223966
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|211435357|gb|FL223965.1|FL223965
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|211437953|gb|FL223979.1|FL223979
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|60350205|gb|DN217178.1|DN217178
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|32912474|gb|CF017286.1|CF017286
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|60355210|gb|DN222183.1|DN222183
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
EST: gi|4887407|gb|AI677506.1|AI677506
EST:     CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATC                         GAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC
genomic: CCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTC

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: 43 (upstream exon), 43 (downstream exon)
Score: 41

GGTTCTCGCCGGTAGGCGGCGCAGGTGGAGCACGCTCGTGGTCTGCGCGGCCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTCAGCCCAATGAAGACACCATTACCGCATCCGTTACCAGCTGATGATCCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 120

GGTTCTCGCCGGTAGGCGGCGCAGGTGGAGCACGCTCGTGGTCTGCGCGGCCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTCAGCCCAATGAAGACACCATTACCGCATCCGTTACCAGCTGATGATCCTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 72

GGTTCTCGCCGGTAGGCGGCGCAGGTGGAGCACGCTCGTGGTCTGCGCGGCCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTCAGCCCAATGAAGACACCATTACCGCATCCGTTACCAGCTGATGATCCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

GGTTCTCGCCGGTAGGCGGCGCAGGTGGAGCACGCTCGTGGTCTGCGCGGCCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctct ... ttgttgctagGAATGGGAGAGACCAAAGCCTGGGAGGAGACCTGATATCTTCCCTAAGTTCAGCCCAATGAAGACACCATTACCGCATCCGTTACCAGCTGATGATCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCTCGCCGGTAGGCGGCGCAGGTGGAGCACGCTCGTGGTCTGCGCGGCCCCCGACGAGGAGAAGATTACCAAGCGGTCGCCCCTCGATTTCCCCATCgtaattctcttgctcttcaacttaccatcggttcatttcattttagcagcttgttctggtgggattggaggaggctataggctgcccaataaccggttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA