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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgttttgtgaatagactgcttttgatttgtttcctagctctgttgtagatgtaccccaggattgttgatttctggtaattggttggttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG

Basic information

species Zea mays
transcript GRMZM2G427097_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G427097_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 3'ss of exon 6
gttttgttttgtgaatagactgcttttgatttgtttcctagctctgttgtag-atgtacccc-aggattgttgatttctggtaattggttggttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG
   ||   |  |||| |  ||  |||   |   | | |||| ||    |||| ||| |||   |  |   | |     |   |  |  ||| | ||  | ||||| |||||||| || ||||||||||||||| |||| ||||||||||| ||||||||||||||||| || ||||||
--gttacatgttgaagaacctattttatctgattattctagttcaacagtagtatgcaccaagaaaaaaatagccaatttacatataattgatcttctgaagGGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAG

upper sequence: GRMZM2G427097_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv00s1491g00010.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------gttttgttttgtgaatagactgcttttgatttg------tttcctagctctgttgtagatg---taccccaggattgttgatttctggtaattggttg----gttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG
                                                      | |||    |||  |    ||| |  |  |       | || ||  | ||      ||    ||  | |    ||||   |||| |   |   ||      | ||||  |||||||||||  |  | || || || |||||| |||| |||||||| || ||||| |||||||||||||| ||||||
gttcatgaatgtgatgtcctcattccatgcgcattaggtggagttctcaacaagtatgtgacatgaccacttagctgtgaaccttataaactctcatatttttgggtccaataacttaatcaaactatgtttccttcttgccctgcattctgatatattgcaaagGGATAATGCTGCTCATGTTAAAGCAAAATTTATAATAGAAGCTGCAAATCATCCCACTGATCCAGAGGCTGACGAG
















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|20300129|gb|BQ163072.1|BQ163072
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|71758196|gb|DR956133.1|DR956133
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|89763860|gb|DY690877.1|DY690877
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCTTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATGGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|27521989|gb|CA989095.1|CA989095
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCGCCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|19351691|gb|BM896223.1|BM896223
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|19351384|gb|BM895916.1|BM895916
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|18384257|gb|BM417456.1|BM417456
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|8367160|gb|BE050105.1|BE050105
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAAT
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAAT
EST: gi|60395163|gb|DN228032.1|DN228032
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|18384249|gb|BM417448.1|BM417448
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|71769690|gb|DR967627.1|DR967627
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|87151934|gb|DY396723.1|DY396723
EST:     TGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: TGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|71762903|gb|DR960840.1|DR960840
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATGGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|19272553|gb|BM888809.1|BM888809
EST:     GTGGAGCTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: GTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|148950840|gb|EC896455.2|EC896455
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|211086894|gb|FL471058.1|FL471058
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|76933851|gb|DV173611.1|DV173611
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|87152706|gb|DY397495.1|DY397495
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|32944867|gb|CF049686.1|CF049686
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|148938395|gb|EC882709.2|EC882709
EST:     GGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTACCCA
genomic: GGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|22490092|gb|BU050015.1|BU050015
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|76284086|gb|DV023654.1|DV023654
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATGGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA
EST: gi|94472525|gb|EB701483.1|EB701483
EST:     CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAA                         GGATAATGCACCAGACGTGAAGGCCAAATTTGTAATGGAAGCTGCTAACCA
genomic: CATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCA

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: 103

TGAAAGACTTCGATGGTGCGGAAGTTTTGGATTCAACCGAGTTGTTAGTGCATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 930

TGAAAGACTTCGATGGTGCGGAAGTTTTGGATTCAACCGAGTTGTTAGTGCATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 880

TGAAAGACTTCGATGGTGCGGAAGTTTTGGATTCAACCGAGTTGTTAGTGCATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

TGAAAGACTTCGATGGTGCGGAAGTTTTGGATTCAACCGAGTTGTTAGTGCATGACTGTGATGTTCTTGTCCCCTGCGCCTTAGGTGGAGTTCTTAACAAgtaagaacca ... ttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtagatgtaccccaggattgttgatttctggtaattggttggttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG
                     tgttgat  putative branch site (score: 189)
                       ttgattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgttttgtgaatagactgcttttgatttgtttcctagctctgttgtagatgtaccccaggattgttgatttctggtaattggttggttttgcgcagGGATAATGCACCAGACGTGAAGGCCAAATTTGTAATCGAAGCTGCTAACCATCCAACTGATCCAGAGGCAGACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - tgttttg
- - - - - - - - - -ctgcttt
- - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - -gatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggttg