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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttgtgatttgctagttttgttatttcttgtggttgatgattcatcatgttctactttttctttgctaaggttactgatattcttaatttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC

Basic information

species Zea mays
transcript GRMZM2G041797_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 1
-gtgttgtgatttgctagttttgttatttcttgtggttgatgattcatcatgttctactttttctttgctaaggttactgatattcttaatttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC
  ||||   | ||||| || |  ||  |   | |   |  |||||   | | |  |   |  |      | || | ||  |  |  ||  |||||   |||||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||
tatgtttgaaattgcttgtgtatttgataactttttattttgattttacttatgttgggtactaagattttag-tcaccaaattcattcttttcttttcagCACTTCGTTTTGGAGGAGAACATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTGTTGAAGGCATCGGGGCATGTCGAGAAGTTTACTGACC

upper sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 1
gtgttgtgatttgctagttttgttatttcttgtggttgatgattcatcatgttctactttttctttgctaaggttactgatattcttaatt-tctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC
 ||      | | | | |  ||  || | | |||  |||  ||  |  ||    |||  || |||||      ||  ||||   ||  ||| | |   ||||| |||||| | || ||||| |||||||| ||||||||||| ||||| |||||||| |||||  ||||||| || || ||||| || || ||||| ||||
-tgcacatttatacgaatgctggcatatgtagtgcatgaatatataaaattcaatacaattcctttgaatgtattgttgatccactctattcttttttcagCATTTTGTTCTTGAGGAGAACATGTTGGAAGTTGACTGCCCTTGTGTAACGCCTGAAGTTGTTCTGAAGGCTTCAGGGCATGTTGATAAATTTACCGACC

upper sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 1
--gtgttgtgatttgc-tagttttgttatttcttgtggttgatgattcatcatgttctactttttctttgctaaggttactgatattcttaatttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC
    | | |  ||  | |   ||| | | | |  |||       |      |   |||     || ||||       |  |    |  || || |     ||||| |||||| |||| |||||||||||||| ||||| ||||| |||||||| || ||  |||| |||||||||||||| ||||| || ||||| ||||| |
taaagctctagttatcgtgaatttttaagtgcgcgtgagcatgcacatgggagtctctgtgcattttttgt---aactgatcccctcttttatattgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACACCAGAAATTGTATTGAAGGCATCGGGTCATGTTGATAAGTTCACTGATC

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|18649594|gb|BM498413.1|BM498413
EST:     GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTAACG
genomic: GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG
EST: gi|87152971|gb|DY397760.1|DY397760
EST:     GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTAACG
genomic: GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG
EST: gi|33100212|gb|CF060172.1|CF060172
EST:     GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG
genomic: GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG
EST: gi|93284057|gb|EB676321.1|EB676321
EST:     CTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG
genomic: CTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG
EST: gi|18450658|gb|BM428936.1|BM428936
EST:     GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTAACG
genomic: GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG

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: 47 (upstream exon), 48 (downstream exon)
Score: 169

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 123

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 65

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 149

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatgttctactttttctttgctaaggttactgatattcttaatttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC
                                     ttcttaatttctcccc  CT-rich tract
                                tgatattcttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttgtgatttgctagttttgttatttcttgtggttgatgattcatcatgttctactttttctttgctaaggttactgatattcttaatttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - tgtgatt
- - - - - - - - -ttttgtt
- - - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgat