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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtcccattccaagtgtattcgatctgatttttagatcaaacacattcacccgcctttattagaaaggttaacgaaagcccaggatccaccgctggg...

Basic information

species Zea mays
transcript GRMZM2G574782_T01
intron # 3
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 3
lower sequence: LOC_Os11g29370.1 (Oryza sativa), 5'ss of exon 3
GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtcccattccaagtgtattcgatctgatttttagatcaaa---cacattcacccgcctttattagaaaggttaacgaaagcccaggatccaccgctggg
|| |||||||||||||||||||||||||| ||||| |||||||| || || |||||||| ||||| |||||    ||||||||||| ||||| || || |  ||  ||     | | |||    ||| | |||| | |     ||  |   |      ||  |    | |||| |               |  |  |  
GCTTATCTGATGAGAGGAGCTGGGGCTGTTATTCATAGCCATGGGATGGAAACTTGCATTGCAACCATGCTTGATCCTGGTGCAAAAGAGTTTAGGgtgaacccacttgtc--tcttttccccatgaatcttagctaatgttccagttctgctttatatttctcatgaagttagctgtgatgtttacaaaaatgtggt-
















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:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|76289240|gb|DV028808.1|DV028808
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|211266802|gb|FK955969.1|FK955969
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|211264368|gb|FK955956.1|FK955956
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCACA                         GTGACCCACATGGAAATGATCAAAGGAAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAAT
EST: gi|21809578|gb|BQ667896.1|BQ667896
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|211266798|gb|FK955965.1|FK955965
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGAT
EST: gi|148938308|gb|EC882615.2|EC882615
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAAGAGTTCAGA                         GTGACCCCACCTGGGAATTGATCAAAGGA
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCC-ACATGGAAAT-GATCAAAGGA
EST: gi|211266801|gb|FK955968.1|FK955968
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCA
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCA
EST: gi|32862805|gb|CF002487.1|CF002487
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|148939493|gb|EC884073.2|EC884073
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|8368441|gb|BE051386.1|BE051386
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|148956120|gb|EC901887.2|EC901887
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|31359134|gb|CD443491.1|CD443491
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCANAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|20507404|gb|BQ279616.1|BQ279616
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GCGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|6021244|gb|AW066172.1|AW066172
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|148939957|gb|EC884685.2|EC884685
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|60351211|gb|DN218184.1|DN218184
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|91876905|gb|EB406862.1|EB406862
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|26456641|gb|CA828224.1|CA828224
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|148957566|gb|EC903663.2|EC903663
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|211266806|gb|FK955973.1|FK955973
EST:     CATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: CATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|211264372|gb|FK955960.1|FK955960
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACC
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACC
EST: gi|12967932|gb|BG264879.1|BG264879
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|149079628|gb|EE168621.2|EE168621
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|149079514|gb|EE168492.2|EE168492
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
EST: gi|211266805|gb|FK955972.1|FK955972
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATG
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATG
EST: gi|109179163|gb|EC379844.1|EC379844
EST:     TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGA                         GTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT
genomic: TAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGAT

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), 46 (downstream exon)
Score: 257

GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 497

GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 581

GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 176

GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtccca ... cttattgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTATCTGATGAGAGGAGCTGGGGCTGTCATTCACAGCCATGGAATAGAGACTTGCATCGCAACAATGCTCATCCCTGGTGCAAAGGAGTTCAGAgtaagtcccattccaagtgtattcgatctgatttttagatcaaacacattcacccgcctttattagaaaggttaacgaaagcccaggatccaccgctggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaccgc