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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccag

Basic information

species Zea mays
transcript GRMZM2G171435_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctcgttt----------tttatcctaccaaatgtgcgtgtat-atatatctttccag
||||||||| || || |||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||| || || |||||||||||||||||  |  |      | |||| |||| | ||| ||||  || ||   ||          || |||  || || ||     || | ||    ||||| ||
TATTTTAACCCCAACTCATCTTGCTATTGTCATGGAATATGCCTCTGGTGGTGAGCTTTTCGAGAGAATTTGTAAGAATGTACGGTTCAGTGAAGATGAGgtacgcaccatttccctggtgcatcct-ctttttgatgcatctttcttgagtgacatattgatcgcactaattgcatcggtctgattctactttctag

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G20610.4 (Glycine max), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccac-ttggttcatctttcttcttgacacacctcgttt---tttatcctac-caaatgtgcgtgtatatatatctttccag
 ||||||||||| || |||||||||||||| ||||||||||| ||||| || ||||| ||||||| ||| || ||    | ||| || |  || |||||||||  |  ||      ||   | ||  | |  ||  |  |     ||||    |||| |||| | | | ||        | |     | |||
AATTTTAACACCTACTCATCTTGCTATTGTAATGGAATATGCATCTGGGGGAGAGCTCTTTGAGAAAATCTGCAATGCTGGGCGTTTTACCGAGGATGAGgttcttatttaatttgtttacttattctacacctgaatgctataagtttgtacttattctacgctagtttgtaacccgttgttatgattcag

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G33120.1 (Glycine max), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttat-cctaccaaatgtgcgtgtatatatatctttccag
||| || || || || ||| | || ||||| ||||||||||| ||||| || ||||| |||||||||||||| ||    |   | |||||||| |||||||||  |   |    |    |||||   | |   | |  |     | | | ||| |||   |  | ||  | |   | |||  | |   
TATATTGACCCCAACACATTTAGCAATTGTGATGGAATATGCTTCTGGAGGAGAGCTATTTGAGAGAATATGCAATGCAGGAAGGTTCAGTGAGGATGAGgttcttatcttttgc---attcattcatttgtgtaatgc----tgctgtatatgccttttatgtctgttttttgttttatgctgcag-

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccag
|||||||||||| || ||||| || ||||| ||||||||||| ||||| || || || ||||||| ||| || ||    | ||| || | ||| |||||||||  |   | | | ||| ||  | || ||| |     | |    |||  | |   || |      | |    ||    |       
TATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAACTATTTGAGAAAATCTGCAATGCAGGGCGTTTTAATGAGGATGAGgttctta--tacaatttgtttacttttgcttgtgctagctctctatttcctgtgtaactattaacccattgtcatgccacag-----

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G09460.1 (Glycine max), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttg------ccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccag--------
 ||||||||||| || |||||||||||||| ||||||||||| ||||| || ||||| ||||||| ||| || ||    |  || || | ||| |||||||||  |  ||         ||||| |  |    |   | | | |    |    ||  |   |      |  ||  || | ||     ||            
AATTTTAACACCTACTCATCTTGCTATTGTAATGGAATATGCATCTGGGGGAGAGCTCTTTGAGAAAATCTGCAATGCTGGACGTTTTACTGAGGATGAGgttcttatttaatttgtttacttgttctacacctgaacgttataagtttgtacttcgaatttgttccctacgcaagtttgtaacctgttgttatgattcag

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G15330.1 (Glycine max), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccag
||| || ||||| || ||| | || ||||| ||||||||||| ||||| || ||||| |||||||||||||| ||    | | | |||||||| |||||||||  |   ||   |    |||||   | |   | |  |  ||   | |   |  ||     |||  || | | | |||  | |   
TATATTGACACCAACACATTTGGCAATTGTGATGGAATATGCTTCTGGAGGAGAGCTATTTGAGAGAATATGCAATGCAGGGAGGTTCAGTGAGGATGAGgttcttatctgttgc---attcattcatttgtgtaatgctgctgcatatgcctttta-----tgtctgtttttttttatgctgcag-

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G06250.1 (Glycine max), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctc-gttttttatcctaccaaatgtgcgtgtatatatatctttccag
 ||||||||||| || ||||| || ||||| ||||||||||| ||||| || ||||| ||||||| ||| || ||    | ||  || | ||| |||||||||  |      || || ||| |  |||  |  ||  |    ||  |||  | |   || |      | |  |||| |  |       
CATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttata---caatttgtttactttttcttgtgctaggtttctatttcctgtgtaactattaacccattgatatgtcacag-----

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccag
 || |||||||| |||||||| |||||||| |||||||||||  |||| || |||||||||||  | ||||| |||   | ||| |||| ||| |||||||||  || || | ||    |   | |||  | ||     |  |  | |  |||         |    |    |   |   | | |||
CATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATGAGgttcttgatt-caacccattgggttttttctttt---ctagtttttgtgctatttccatggtttcttgacactggttgcttctgcag

upper sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 3
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccag
||| || ||||| ||||| ||||||||||| ||||||||||||||||| || ||||| |||||| | ||||| ||   ||  || |||||||| |||||||||  |   ||| |||||  |||| |   ||  ||  || |  |      |    ||     |   | | | ||  |     | |||
TATATTGACACCAACCCACCTTGCTATTGTGATGGAATATGCCTCTGGAGGAGAGCTCTTTGAGCGGATATGCAATGCCGGCCGGTTCAGTGAGGATGAGgttctta--tgcaacttg-ctcatttggttttctgttactctcctcgcactcgtttatggcttac-cttctctagcttgtactgcag

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|211022079|gb|FL377464.1|FL377464
EST:     GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG                         GCTCGCTACTTCTTCCAACAACTCAT
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCAT
EST: gi|211499753|gb|FL295241.1|FL295241
EST:     GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG                         GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST: gi|211499759|gb|FL295247.1|FL295247
EST:     GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG                         GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST: gi|6022633|gb|AW067445.1|AW067445
EST:     GNGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG                         GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST: gi|148932906|gb|EE285698.2|EE285698
EST:     GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG                         GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST: gi|211204702|gb|FL178018.1|FL178018
EST:     GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG                         GCTCGCTACTT
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTT
EST: gi|78107855|gb|DV526273.1|DV526273
EST:     GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG                         GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST: gi|211108565|gb|FL429107.1|FL429107
EST:     GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG                         GCTCGCTACTTCT
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCT

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: 101

TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 84

TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG