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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctcgacaaagattgcacctttagtcgattgtttgtcttctcatttcttctgttccttccatttcatttgattggactcatcttttccag

Basic information

species Zea mays
transcript GRMZM2G007381_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007381_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 5'ss of exon 3
GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttt-tctcgacaa-agattgc--------------acctttagtcgattgtt---tgtcttctcatttcttctgttccttccatttcatt------tgattggactcatcttttccag
|||||| ||||||||||||||||||||||| || |||||||||||| | |||||| ||||||| |||||||||||||||||||| |||||||| ||||||||  | ||| | |  |||| ||||| |              ||||||| |  ||  ||   | ||||||||| | |||  | | ||| ||||  ||      | |||  |||| |   ||||||
GGTAATCGAGGTCACCGGAGCGGCGGGCACGCTCTACGCCGGCGAGACATACCAGCTGCAGGTCGACTTCCCTGAGCATTATCCCATGGAGGCGCCTCAGgtgagctttcttttcacaacagattactttctcatatagaaacctttaattaatcctttcgtttcttctcatctgttccctgcattcgatttggttgcaaactaatttaactctttcattccag

upper sequence: GRMZM2G007381_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT4G36410.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctcgacaaagattgcacctttagtcgattgtttgtcttctcatt--tcttctgttccttccatttcatttgattggactcatcttttccag
| | ||||| ||    ||||   | || || |||||||||   ||  |||||||  | || ||||| ||||||||||||||||||||||| || || |||||  | |  |||         |   |    |   ||||  ||  || || |||   |||  |   ||     || ||  | ||   ||             
GATCATTGAAGTGCATGGAGTTCCAGGAACTCTTTACGCCAATGAAACTTACCAACTTCAAGTTGAGTTCCCTGAGCATTATCCTATGGAAGCTCCACAGgttcg-tcctctaactccttttgttaatacttaacgatacttaatcatcgcatcaatctcataacccgatggttccacat-ataaaacag-----------
















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|211242854|gb|FL389165.1|FL389165
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAACCCACCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|71431746|gb|DR812796.1|DR812796
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|211172115|gb|FK994020.1|FK994020
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|45846873|gb|CN070816.1|CN070816
EST:     AGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCCACGGG
genomic: AGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|50331624|gb|CO526750.1|CO526750
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|211172114|gb|FK994019.1|FK994019
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|116827090|gb|EC870952.1|EC870952
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|17931977|gb|BM268937.1|BM268937
EST:     GGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: GGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|78081936|gb|DV510348.1|DV510348
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|71431745|gb|DR812795.1|DR812795
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|16925448|gb|BM078516.1|BM078516
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|18165814|gb|BM335659.1|BM335659
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAGCGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|211215511|gb|FL424481.1|FL424481
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAACGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|29946817|gb|CB816340.1|CB816340
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|22819231|gb|BU499321.1|BU499321
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|16919478|gb|BM074211.1|BM074211
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|211172116|gb|FK994021.1|FK994021
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|29945777|gb|CB815814.1|CB815814
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|211172113|gb|FK994018.1|FK994018
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
EST: gi|211172112|gb|FK994017.1|FK994017
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGG

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: 221

GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGGCACATCTGCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 507

GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGGCACATCTGCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 636

GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGGCACATCTGCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 370

GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... tcttttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATTTACAGCAACGGGCACATCTGCTTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAATTGAGGTCACCGGAGCGGCGGGCACCCTTTACGCCGGCGAGGCTTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggttttctcgacaaagattgcacctttagtcgattgtttgtcttctcatttcttctgttccttccatttcatttgattggactcatcttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG