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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaatgctccctcctttttaatttttctgttgcttctgcttgttttgatctgaaaactctagtttcctttggtgttttgaag

Basic information

species Zea mays
transcript GRMZM2G574782_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g29370.1 (Oryza sativa), 5'ss of exon 2
TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaatgctccctcctttttaatttttctgttgcttctgcttgttttgatctgaaaactctagtttcctttggtgttttgaag
|||| || | ||||||||||| ||||| ||  | |||||| ||||||||||||||||||||||||| || || || |||||||||||||||||||||||||||  | | ||||  |   |  ||||||| || |   ||||  ||||||||  ||| ||   |||| ||| | ||||| ||||| ||
TGTGCTGTCAGCAGATGGGAAGGTGCTCTCCTCACCTGTATCAAAGCCATGGCCAAACAAGCCTCCAAAATGTACTGACTGTGCTCCTCTGTTCATGAAGgtt-atcagtgctatcctttgcttaatttgtccg---cttcaacttgttttagtctaaattgtctaattttcattggtattttgcag

upper sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G53850.3 (Arabidopsis thaliana), 5'ss of exon 2
TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaatgctccctcctttttaatttttctgttgcttctgctt-----gttttgatctgaaaactctagtttcctttggtgttttgaag----------
  |  |  ||||  ||||     |  | ||| | ||     |||||||||  ||||| |||||||| ||||| || || |||||||| || ||||||||||| ||    ||   | | |    || |  | |  ||| |||||| |      |||   | |    |   |  ||  |  |    | |||             
CATCTTATCTGCTAATGGATCCATCATATCTACACCCTCTCCAAAGCCATACCCAAATAAGCCTCCCAAGTGTACCGATTGTGCTCCACTTTTCATGAAGgtatggttttgtcgctttcaaggtagtaatac--ttgattctgcgttagggatttctgtatacgtagcttgattatcactttgctattggccttctttatct

upper sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ34464 (Selaginella moellendorffii), 5'ss of exon 2
TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaatgctccctcctttttaatttttctgttgcttctgcttgttttgatctgaaaactctagtttcctttggtgttttgaag
|||| ||| |    |||||   || || ||  | ||  |  ||  |||    ||  ||||||| || || |||||||||||||||||||| ||||||||||||    || ||| | ||  ||||| ||||| | ||  |  | ||| |  |||       | ||  |  |                 
TGTGCTGGATAAGAATGGGGCCGTCCTCTCCACACCACTGCCATTGCCTCCTCCTCACAAGCCGCCCAAATGCACGGACTGTGCTCCTCTTTTCATGAAGgttct--aaagcttcttc--ttttacttttttttttattctttcttctcatgagacttggattcgtgacttag--------------

upper sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ05817 (Selaginella moellendorffii), 5'ss of exon 2
TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaatgctccctcctttttaatttttctgttgcttctgcttgttttgatctgaaaactctagtttcctttggtgttttgaag
|||| ||| |    |||||   || || ||  ||||  |  ||  |||    ||  ||||||| || || |||||||||||||||||||| ||||||||||||    || ||| | ||  || || ||||| |      |    |  || | ||  ||      | | |||     |||  ||    
TGTGCTGGATAAGAATGGGGCCGTCCTCTCCACGCCATTGCCATTGCCTCCTCCTCACAAGCCGCCCAAATGCACGGACTGTGCTCCTCTTTTCATGAAGgttct--aaagcttcttc--ttgtacttttttttaaaaattctttccttctcatgcga----cttggattc-----gtgacttag--

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|148973039|gb|EE024097.2|EE024097
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|76289240|gb|DV028808.1|DV028808
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCATAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|211266802|gb|FK955969.1|FK955969
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|211264368|gb|FK955956.1|FK955956
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|21809578|gb|BQ667896.1|BQ667896
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|211266798|gb|FK955965.1|FK955965
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|148938308|gb|EC882615.2|EC882615
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|211266801|gb|FK955968.1|FK955968
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|148939493|gb|EC884073.2|EC884073
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|8368441|gb|BE051386.1|BE051386
EST:     TGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: TGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|148956120|gb|EC901887.2|EC901887
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|31359134|gb|CD443491.1|CD443491
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|20507404|gb|BQ279616.1|BQ279616
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|6021244|gb|AW066172.1|AW066172
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGNCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|148939957|gb|EC884685.2|EC884685
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|60351211|gb|DN218184.1|DN218184
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|91876905|gb|EB406862.1|EB406862
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|26456641|gb|CA828224.1|CA828224
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|148957566|gb|EC903663.2|EC903663
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|211264372|gb|FK955960.1|FK955960
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|12967932|gb|BG264879.1|BG264879
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|149079628|gb|EE168621.2|EE168621
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|149079514|gb|EE168492.2|EE168492
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
EST: gi|211266805|gb|FK955972.1|FK955972
EST:     GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAG                         GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG
genomic: GGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAG

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: 386

TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 793

TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 923

TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaat ... tgttttgaagGCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGATGGCTGCAGATGGGAAAGTGCTTTCTGCGCCTGTAGCAAAGCCATGGCCAAACAAGCCTCCTAAGTGCACGGACTGTGCTCCTCTGTTCATGAAGgtttgtgaatgctccctcctttttaatttttctgttgcttctgcttgttttgatctgaaaactctagtttcctttggtgttttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC