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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactctttcatactgaacctttttttgttaataccattgtcagtcactcagttagttggttccatttttctcatcttgatgcttcagctgatctggctttgtttggttatgtacag

Basic information

species Zea mays
transcript GRMZM2G150251_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA14G21190.1 (Glycine max), 5'ss of exon 3
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactctttcatactgaacctttttttgttaataccattgtcagtcactcagttagttggttccatttttctcatcttgatgcttcagctgatctggctttgtttggttatgtacag
| |||||| ||||| ||||||||||||||||| |||||||||||||| |||||||| || || ||||| ||||||||||| |||||||| | || | |     | | |   |||| || ||  || | | ||  |    | |  |  ||  |   | |    | ||   ||  ||  ||    ||| | ||                 
GCTGGACTCTTTGTTTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttaacattttaatgaaataa---ttttatttttcctatcttcgtgtgaagtttaaatgtttaat---actcccttgattgcgaaactgtagactttcttgtttaa---------------

upper sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA06G08620.3 (Glycine max), 5'ss of exon 8
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactctttcatactgaacctttttttgttaataccattgtcagtcactcagttagttggttccatttttctcatcttg--atgcttcagctgatctggctttgtt-tggttatgtacag----------
| ||| || ||||||||||||||||||||||| |||||||||||||| ||||| || || || ||||| ||||||||||| |||||||| |    | || |  |   ||      ||| |   |  | ||||  |    | | ||   |  || |  |  | |||  |    |   |  |    ||||     |  | | || ||  | |           
GCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACTCCAGTGATGGTTAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttaagttttttgctaatgaaatggagatttctgtttgtctttgtgtgaattttaattgtatatttactatgatatcagataagaaaaatgtaataaatctattcctaatattgtcattcaaattattttgcag

upper sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 8
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactctttcatactgaacctttttttgttaataccattgtcagtcactcagttagttggttccatttttctcatcttgatgctt-cagctgatctggctttgtt-tggttatgtacag----------
| ||| || ||||||||||||||||||||||| |||||||| ||||| |||||||| || || ||||| ||||||||||| |||||||| ||   | || |  |   ||      ||| |   |  | ||||  |    | | ||   |  || |  |  | |||  |  |    |  |    ||||     |  | | || ||  | |           
GCTGGTCTATTTGTGTATGACATTTTCTGGGTTTTCTTCACCCCAGTGATGGTCAGCGTTGCAAAATCATTTGATGCTCCAATAAAGgttagtttttttgctaatgaaatggagatttctgtttgtctttgtgtgaattttaattgtgtacttactatgatatcagataaaaaaatgtaataaatctattcctaatattgtcattcaaattattttgcag

upper sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 5'ss of exon 7
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactctttcatactgaac-ctttttttgttaataccattgtcagtcactcagttagttggttccatttttctcatcttgatgcttcagctgatctggctttgtttggttatgtacag
|  ||||| ||| | ||||| || |||||||| ||||| |||||||||||||| ||||| || ||||| || |||||||| || ||||| || |    | | |    |   |      |   ||    ||| | | |   ||  |||||   ||   |||   | ||||   || | ||    || |   |  |               
GCAGGACTATTTTTCTATGATATCTTCTGGGTTTTCTTTACTCCAGTTATGGTTAGTGTTGCCAAATCCTTCGATGCTCCAATTAAGgttagtaaaaatgcctcaaaagtacacaccataccaaattgattctgatttgttc--ttagtcaatt---tttcagtaatctcattgttacat---atttctttcag---------------

upper sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 8
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagc-actctttcatactgaacctttttttgttaataccattgtcagtcactcagtt-agttggttccatttttctca-tcttgatgcttcagctgatctggctttgtttggttatgtacag-----------------
|  ||||||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| || || || || ||||||||||| ||||||||  |  |      |||||    ||  |  |  |||   | ||   |   ||| || | || | ||  || |  | | || | | | || |  |  | |    || |     ||   ||||                 
GCAGGACTTTTTGTTTATGATATTTTCTGGGTCTTCTTCACTCCAGTGATGGTCAGTGTTGCAAAGTCCTTCGATGCTCCTATTAAGgtcagttatccaggtcaactgagatattaatcctggatattctggtttttggttcaatttatttcgctctgttgtaattaatcattaagtttaatttactttattattctaaatgtaataacagttcaattctttttgcag

upper sequence: GRMZM2G150251_T01 (Zea mays), 5'ss of exon 8
lower sequence: EFJ18240 (Selaginella moellendorffii), 5'ss of exon 7
GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactctttcatactgaacctttttttgttaataccattgt-cagtcactcagttagttggttccatttttctcatcttgatgcttcagctgatctggctttgtttggttatgtacag
|  || || || || |||||||| |||||||| ||||||||||| || |||||||  || || || || ||||||||||| || |||||  |  |||| |||     |  | |  ||   |||| ||    | |||                                                                         
GCCGGGCTATTCGTATATGACATCTTCTGGGTATTCTTCACTCCTGTGATGGTCACCGTTGCGAAGTCCTTTGATGCTCCCATCAAGgtttg--ctctctcagtgcaatgcatccttctctaatccctccatgcag-------------------------------------------------------------------------

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|33092200|gb|CF052194.1|CF052194
EST:     TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCGATAAAG                         CTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
genomic: TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
EST: gi|33093608|gb|CF053602.1|CF053602
EST:     TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCGATAAAG                         CTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
genomic: TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
EST: gi|78123104|gb|DV541488.1|DV541488
EST:     TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAG                         CTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
genomic: TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
EST: gi|32837706|gb|CD977384.1|CD977384
EST:     TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCGATAAAG                         CTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
genomic: TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
EST: gi|76282340|gb|DV021908.1|DV021908
EST:     TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAG                         CTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT
genomic: TCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTT

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: 82

GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTTGGTGACATTGTAATACCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTTGGTGACATTGTAATACCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTTGGTGACATTGTAATACCTG


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

GGTGGACTTTTTGTGTATGACATTTTCTGGGTGTTCTTCACTCCAGTTATGGTCAGTGTGGCTAAATCTTTTGATGCTCCTATAAAGgtcagcactc ... ttatgtacagCTTCTGTTTCCTACTGCGGATGATGCACGGCCATTCTCCATGCTTGGCCTTGGTGACATTGTAATACCTG