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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatatggtatcgtcattaaaacaaagaagagttatggctctattttttgagtttagtcttagcgtcaattttttttttgttgaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT

Basic information

species Zea mays
transcript GRMZM2G177631_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 12
gtaaatatatggtatcgtcattaaaacaaagaagagttatggctctattttttgagttta-gtcttagcgtcaattttttttttgttgaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT
              |   |||||         | | || ||     || || |||||||  |||| |   | |  |  |||||  || ||| ||||||| |||||||| || ||| | ||||||||| | ||||||||||| || |  || || |||||||| |||||||| |||||||| ||||||||||| ||||
-------------gtaagcattattgtgctacataattttg---tgatcttctgagtttctgtctgaatcttacatcatttttatttcaaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT
















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|32848162|gb|CD987843.1|CD987843
EST:     ACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTGGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: ACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|32928702|gb|CF033514.1|CF033514
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTGGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|32928613|gb|CF033425.1|CF033425
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTGGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|32928987|gb|CF033799.1|CF033799
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTGGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|211063664|gb|FL415621.1|FL415621
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|32928305|gb|CF033117.1|CF033117
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTGGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|67031384|gb|CO460133.1|CO460133
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTGGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|211489038|gb|FL096937.1|FL096937
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|211366969|gb|FL429347.1|FL429347
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
EST: gi|76285795|gb|DV025363.1|DV025363
EST:     GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAG                         CTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC
genomic: GTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCC

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: 47 (upstream exon), 49 (downstream exon)
Score: 264

TATCAACTCCATCGTTTATCCCTGGACGTCCATTCCTCTCCTGGCTTACTGTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 305

TATCAACTCCATCGTTTATCCCTGGACGTCCATTCCTCTCCTGGCTTACTGTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 406

TATCAACTCCATCGTTTATCCCTGGACGTCCATTCCTCTCCTGGCTTACTGTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 385

TATCAACTCCATCGTTTATCCCTGGACGTCCATTCCTCTCCTGGCTTACTGTACCTTGCCTGCCATCTGCCTGCTCACGGGGAAGTTTATCACACCAGAGgtaaatatat ... gaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctattttttgagtttagtcttagcgtcaattttttttttgttgaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT
                                ttttttttttgttg  CT-rich tract
                            tcaattttttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatatggtatcgtcattaaaacaaagaagagttatggctctattttttgagtttagtcttagcgtcaattttttttttgttgaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG