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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttctgctcgcaacacgacaaatataatgatgcgttgctttgtgtaacttgatcctcccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTTGCTTACGCACGACACAAGGGGCTCGTCGGATCCTGAATAGCTGAAATAA

Basic information

species Zea mays
transcript GRMZM2G159295_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159295_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 10
gtaggtttctgctcgcaa----------cacgacaaatataatgatgcgttgct-------ttgtgtaacttgatcctcccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTTGCTTACGCACGACACAAGGGGCTCGTCGGATCCTGAA--TAGCTGAAATAA
||| ||      |  |||           ||    |||| | ||  || |  ||        |||  |||||  | |   | |||||||||||||| || ||||| ||||| |||||||| || || |||||||||||||| |||||||| |||||||| |||||||| || ||||  | ||  |||   
gtaagtcaaccattacaaaagggtcgtttaccgtcaataaattgtggcctgtctaaccaagctgta-aactttgttcctgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTTGCGTACGCACGGCACAAGGGCCTCGTCGGGTCGTGAACCTTGCCCAAAC--
















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|149107574|gb|EE189456.2|EE189456
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|166675571|gb|EG302253.1|EG302253
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCA
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCA
EST: gi|211202307|gb|FL411327.1|FL411327
EST:     TATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|148945148|gb|EC890346.2|EC890346
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|16917373|gb|BM073255.1|BM073255
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|211426158|gb|FL378594.1|FL378594
EST:     TATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|149105622|gb|EE291166.2|EE291166
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|149102719|gb|EE188266.2|EE188266
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|211426157|gb|FL378593.1|FL378593
EST:     TATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|29544199|gb|CB604579.1|CB604579
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|149107640|gb|EE189521.2|EE189521
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|211094045|gb|FL457288.1|FL457288
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|60337564|gb|DN204537.1|DN204537
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|211311634|gb|FL417536.1|FL417536
EST:     TATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|88756122|gb|DY540263.1|DY540263
EST:     TGAATATTCCGTATACCTGGAATGAGGGCCACGGATACATCTTCAAATGG                         GTGGTTTTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTTTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|5650275|gb|AI920635.1|AI920635
EST:     TGAATATTCCGTATTCCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|37382291|gb|CF628086.1|CF628086
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|149073143|gb|EE161419.2|EE161419
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|14203648|gb|BG837325.1|BG837325
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|88750684|gb|DY534825.1|DY534825
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|76291165|gb|DV030733.1|DV030733
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|12973545|gb|BG268534.1|BG268534
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCAATGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
EST: gi|14243174|gb|BG840819.2|BG840819
EST:     TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGG                         GTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT
genomic: TGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTT

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: 30 (upstream exon), 48 (downstream exon)
Score: 96

TGGTACCGTCTGTCTGTCGCTGTACTCATTAGTTGCTGGAGTCTTTGGTATGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTTGCTTACGCACGACACAAGGGGCTCGTCGGATCCTGAATAGCTGAAATAA


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 241

TGGTACCGTCTGTCTGTCGCTGTACTCATTAGTTGCTGGAGTCTTTGGTATGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTTGCTTACGCACGACACAAGGGGCTCGTCGGATCCTGAATAGCTGAAATAA


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 161

TGGTACCGTCTGTCTGTCGCTGTACTCATTAGTTGCTGGAGTCTTTGGTATGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTTGCTTACGCACGACACAAGGGGCTCGTCGGATCCTGAATAGCTGAAATAA


Block sizes: 30 (upstream exon), 45 (downstream exon)
Score: 235

TGGTACCGTCTGTCTGTCGCTGTACTCATTAGTTGCTGGAGTCTTTGGTATGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttct ... cccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTTGCTTACGCACGACACAAGGGGCTCGTCGGATCCTGAATAGCTGAAATAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacgacaaatataatgatgcgttgctttgtgtaacttgatcctcccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTTGCTTACGCACGACACAAGGGGCTCGTCGGATCCTGAATAGCTGAAATAA
                                    cttgatcctcccttc  CT-rich tract
      acaaatataatgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtttctgctcgcaacacgacaaatataatgatgcgttgctttgtgtaacttgatcctcccttcacagGTGGTTCTTGTATCAGGGCTTTTTTGTGCCTTTATATTTGTCTCCATTGTTGCTTACGCACGACACAAGGGGCTCGTCGGATCCTGAATAGCTGAAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA