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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaactatgtttcttaattagtggcattccatgtttcaattgttttagctaatgatgttatctcttgttcccag

Basic information

species Zea mays
transcript GRMZM2G075153_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075153_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 8
GTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaa----ctatgtttcttaattagtg-gcattccatg---tttcaattgttttagctaatgatgttatctctt----gttcccag--------------
 ||| | || |||||||| ||||||||||||||||||||||| |||||||||||  | |||||  | ||||||||||| ||||||||||| ||||||||||| || |    ||    || | | ||  ||  ||  | |||    | | | |  ||    |  |  |||| | | ||    ||  |                 
CTACTTGATTCTTCGAGGCATGAAGACACTGCATCTCCGTGTACAATGTCAGAATAATACTGCAATGCGGATGGCCCAATTTTTAGAGGAACATCCAAAGgtttgcaaactctgcacttttcatttgttgtacaagctatgaagctacgagtagttctttttgttgtgttgttttttctgagtctcttatttcctatccttag
















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|89248894|gb|DY620680.1|DY620680
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|67012102|gb|CO440851.1|CO440851
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|60395696|gb|DN228566.1|DN228566
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|4804475|gb|AI665345.2|AI665345
EST:     AGAACGACCCTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|9825106|gb|BE575308.1|BE575308
EST:     GAACGACACTGCTCTTCGGATGGCCCANG-TTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: GAACGACACTGCTCTTCGGATGGCCCA-GTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|47962545|gb|CN845254.1|CN845254
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|78122335|gb|DV540719.1|DV540719
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTTTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|88750228|gb|DY534369.1|DY534369
EST:     GTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: GTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|67012003|gb|CO440752.1|CO440752
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|211484408|gb|FL480088.1|FL480088
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|60398293|gb|DN231109.1|DN231109
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|13515896|gb|BG518172.1|BG518172
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|4647443|gb|AI622518.1|AI622518
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|76291941|gb|DV031509.1|DV031509
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|29946122|gb|CB815990.1|CB815990
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|60352254|gb|DN219227.1|DN219227
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|71763831|gb|DR961768.1|DR961768
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|60397682|gb|DN230498.1|DN230498
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|213192843|gb|FM182914.1|FM182914
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|149094738|gb|EE180294.2|EE180294
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTTTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|71419167|gb|DR804675.1|DR804675
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
EST: gi|30705989|gb|CD058994.1|CD058994
EST:     AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAG                         ATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT
genomic: AGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATT

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: 48 (upstream exon), 49 (downstream exon)
Score: 170

GTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATTGCCAAGAGTCAAATGACTGGCTTTGGCGGTGTTGTTAGTTTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 358

GTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATTGCCAAGAGTCAAATGACTGGCTTTGGCGGTGTTGTTAGTTTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 540

GTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATTGCCAAGAGTCAAATGACTGGCTTTGGCGGTGTTGTTAGTTTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 195

GTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaacta ... ttgttcccagATTGCTCGTGTCTACTATCCTGGCTTGCCAAGTCACCCTGAACATCACATTGCCAAGAGTCAAATGACTGGCTTTGGCGGTGTTGTTAGTTTTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGCATCCAAAGgtgtgaactatgtttcttaattagtggcattccatgtttcaattgttttagctaatgatgttatctcttgttcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA