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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATAATAGGTGTCCATCCCCCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatttgttgttgtcagcatctgtagactgagcgaagataacttatcatatatgtctagttgcttttttggtatttttctgttatataggtagaa...

Basic information

species Zea mays
transcript GRMZM2G180815_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g44394.1 (Oryza sativa), 5'ss of exon 9
GCTTATAATAGGTGTCCATCCCCCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatttgttgttgtcagcatc-tgtagactgagcgaagataacttatcatatatgtctagttgcttttttggtatttttctgttatataggtagaa--
||||  |||| |||||| || ||||||||||||||  |||||||||| |||||||| ||||||||||| ||||||||  || | |||   || ||| | |   || |      | ||   || | |  | ||  || ||  ||  | | | | |||||  |  || |  |     
GCTTTCAATAAGTGTCCGTCACCCATCACATGCAGTACATTCAATCAGGATGGCTCAATATTTGCTTATGCGgtaggctatctcttgccatctgcaccataatgaattgttagacatgcattgttacttctga-tactt--ttgctagatttatttctcctggattgtcattcac
















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|84969286|gb|DW467729.1|DW467729
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|91875720|gb|EB405677.1|EB405677
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTTTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|88757959|gb|DY542100.1|DY542100
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|74235194|gb|DT643108.1|DT643108
EST:     CATCACAATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CATCAC-ATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|78073884|gb|DV502318.1|DV502318
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|9254555|gb|BE345023.1|BE345023
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|88758075|gb|DY542216.1|DY542216
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTTTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|91873676|gb|EB403633.1|EB403633
EST:     CCATCCCATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTTTCCTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|50332449|gb|CO527575.1|CO527575
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|211532431|gb|FL471823.1|FL471823
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|78107674|gb|DV526092.1|DV526092
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|71758033|gb|DR955970.1|DR955970
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTTTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|71758084|gb|DR956021.1|DR956021
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTTTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|71432893|gb|DR813943.1|DR813943
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|211532432|gb|FL471824.1|FL471824
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|71763057|gb|DR960994.1|DR960994
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTTTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|29543837|gb|CB604217.1|CB604217
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|76286199|gb|DV025767.1|DV025767
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTTTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|4624367|gb|AI615200.1|AI615200
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA

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: 45 (upstream exon), 49 (downstream exon)
Score: 70

GCTTATAATAGGTGTCCATCCCCCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 14

GCTTATAATAGGTGTCCATCCCCCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG


Block sizes: 44 (upstream exon), 37 (downstream exon)
Score: 10

GCTTATAATAGGTGTCCATCCCCCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 13

GCTTATAATAGGTGTCCATCCCCCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATAATAGGTGTCCATCCCCCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatttgttgttgtcagcatctgtagactgagcgaagataacttatcatatatgtctagttgcttttttggtatttttctgttatataggtagaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagataa