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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaatacaactcaaagcaagcaagcatcagcgccgtcgttgtcttcacaagttctatgagaaggaacggatcggagccttccagagtaacgtacggttcttccatggcatttggtttaatttccag

Basic information

species Zea mays
transcript GRMZM2G152477_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152477_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g13540.1 (Oryza sativa), 5'ss of exon 5
TGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaatacaactcaaagcaagcaagcatcagcgccgtcgttgtcttcacaagttctatgagaaggaacggatcggagccttccagagtaacgtacggttcttccatggcatttggtttaatttccag
 |||  ||||||| |||| || || || |||||||| ||||| |||||||| |||||||||||||||||||| ||||| || || |||||||| ||  ||||     |||||    ||           || |    |   |  |  | |||||     | ||| |    |  |||   |  |    || |  |                                    
AGCGAAGTGGAAGATTGCTGTTGGGCATCATACCATTAGGAGCGTCAGTGACCATGGTGACACCAAGGAGCTTCTGCAACTTCTACTTCCAGTTCTGAAGgtt----atacag---aagttgcctcgatattaagttc--tgaaggatccacaaa----aagagtacttccttatcactgtttcatggaatttcag----------------------------------
















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|37388405|gb|CF631411.1|CF631411
EST:     ACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|148966045|gb|EE016979.2|EE016979
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|16927228|gb|BM080297.1|BM080297
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|76289549|gb|DV029117.1|DV029117
EST:     TCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCCAG                         GCCA-CGGCGTCGATTTCTACATCAACGGGCATGAC
genomic: TCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCC-AGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGAC
EST: gi|32845008|gb|CD984689.1|CD984689
EST:     ATCATGGTGACGCCAAGGAGCTAGTGCAGCTACTGCTTCCAGTCCTACAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|74239383|gb|DT647297.1|DT647297
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         CCCA-CGGCGTCGATTTCTACATCAACGGGCATGAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGAC
EST: gi|37426126|gb|CF650813.1|CF650813
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGG
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGG
EST: gi|32845140|gb|CD984821.1|CD984821
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|32844554|gb|CD984235.1|CD984235
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|50335509|gb|CO530635.1|CO530635
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTTTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|78114010|gb|DV532399.1|DV532399
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|32844045|gb|CD983726.1|CD983726
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|37393857|gb|CF634195.1|CF634195
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|76280616|gb|DV020184.1|DV020184
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GNCCAACG-CGTCGATTTCTA
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagG-CCAACGGCGTCGATTTCTA
EST: gi|71430080|gb|DR811130.1|DR811130
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|76012839|gb|DT940009.1|DT940009
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|78105515|gb|DV523933.1|DV523933
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTTCTCCAG                         GCTCA-CGGCGTCGATTTCTACATCAACGGGCATG
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGC-CAACGGCGTCGATTTCTACATCAACGGGCATG
EST: gi|211405854|gb|FK952121.1|FK952121
EST:     ACTGCTTCCAGTCCTCCAG                         GCCAAC-GSGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|32835913|gb|CD975591.1|CD975591
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|18162089|gb|BM331928.1|BM331928
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTGCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|89758274|gb|DY687518.1|DY687518
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GGCCA-CGGCGTCGATTTCTACATCCACGGGCATGAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagG-CCAACGGCGTCGATTTCTACATCAACGGGCATGAC
EST: gi|71767916|gb|DR965853.1|DR965853
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
EST: gi|76289548|gb|DV029116.1|DV029116
EST:     ATCATGGTGACACCAAGGAGCTACTGCAGTTACTGCTTCCAGTCCTCCAG                         GCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC
genomic: ATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACAC

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: 137

TGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 359

TGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 394

TGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 70

TGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaata ... taatttccagGCCAACGGCGTCGATTTCTACATCAACGGGCATGACCACTGCCTGGAACACATCAGCAGCAGAGACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGCTACTGCAGCTACTGCTTCCAGTCCTCCAGgtatacaatacaactcaaagcaagcaagcatcagcgccgtcgttgtcttcacaagttctatgagaaggaacggatcggagccttccagagtaacgtacggttcttccatggcatttggtttaatttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT