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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggtattgagctcaataccataccaaatgtttttttctctacaatagattattgtattttatatgcattcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG

Basic information

species Zea mays
transcript GRMZM2G107896_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107896_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
aaggtattgagctcaataccataccaaatgtttttttctctacaatagattattgtattttat-atgcattcacttg-gactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG
 |  |  |   ||  ||     |  || || ||| ||   ||     |   ||   ||| | | || | | |||||   ||||| |||||  ||| ||||||||||||||||||||| ||||||||||| |||||||| |||||||| |||||||||||||||||| ||||||| ||||| ||||| ||||
-aattcatagtctatatggagcagtaa-tgatttcttaattatgtctgcaaatgagattatctgattcttccactttcaactgagttgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG

upper sequence: GRMZM2G107896_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
aaggtattgagctcaataccataccaaatgtttttttctctacaatagattattgtattttatatgcattcacttgga--ctgat-ttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG
  ||| ||     || |    |    | |  |||| | | |  ||||| |   | | ||  | |   | | | || |    | ||  | |  | |   |||||||| ||||||||  | | |||||| || | ||| || |||||||| ||||||||||| |||||||| ||||| || || || |||||||
-cggtttttgttgcagtg--gtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG

upper sequence: GRMZM2G107896_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
--aaggtattgagctcaataccataccaaatgtttttttctctacaatagattattgt-attttatatgcattcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG
  ||| | |||       |        | |   ||   ||  |     ||   ||| | |||| | |     | | ||   ||||  ||||  ||   |||||||| ||||||||  | | ||||||||| | ||| || || ||||| |||||||| || |||||||||||||| ||||| || || ||||
ttaagtttttgtttaaggtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaatttcttaatttt-ctgaaatgtt--ttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG

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|22521256|gb|BU080067.1|BU080067
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|91052022|gb|EB162440.1|EB162440
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|101385910|gb|EB815003.1|EB815003
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|61236552|gb|DN586301.1|DN586301
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCCAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|71436668|gb|DR817718.1|DR817718
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|76287872|gb|DV027440.1|DV027440
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|78117243|gb|DV535630.1|DV535630
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|20803428|gb|BQ294478.1|BQ294478
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|91878775|gb|EB408732.1|EB408732
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|71430644|gb|DR811694.1|DR811694
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|89756366|gb|DY686416.1|DY686416
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|32908752|gb|CF013565.1|CF013565
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|211378265|gb|FL111128.1|FL111128
EST:     ACGGCGCGGGAKATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCYTTCATTGACTTCGATG
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCC-TTCATTGACTTCGATG
EST: gi|101384009|gb|EB814059.1|EB814059
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|71429329|gb|DR810379.1|DR810379
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|211380907|gb|FL111133.1|FL111133
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|211380906|gb|FL111132.1|FL111132
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|76014171|gb|DT941341.1|DT941341
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|50326567|gb|CO521693.1|CO521693
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|78081066|gb|DV509478.1|DV509478
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|211380904|gb|FL111130.1|FL111130
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|78113845|gb|DV532234.1|DV532234
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
EST: gi|211378266|gb|FL111129.1|FL111129
EST:     ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA
genomic: ACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGA

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), 48 (downstream exon)
Score: 334

GCTGAACTCATGGCTCGCGTCTTCGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 341

GCTGAACTCATGGCTCGCGTCTTCGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 401

GCTGAACTCATGGCTCGCGTCTTCGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 185

GCTGAACTCATGGCTCGCGTCTTCGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATTGAGGACGAGTTCCGCACGTTTGGGGTTCTGAAGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagattattgtattttatatgcattcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG
                               gactgat  putative branch site (score: 185)
                                     tttgttctttccat  CT-rich tract
     tattgtattttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggtattgagctcaataccataccaaatgtttttttctctacaatagattattgtattttatatgcattcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - ccatacc
- - - - - - - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggactg