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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcgcgacttaatcaattaactgcagtttgcgctgttgcttttcaatttgctataatacttatcctgatcacaactcaaatttcatggtag

Basic information

species Zea mays
transcript GRMZM2G032367_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032367_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 8
ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcgcgacttaatcaattaactgcagtttgcgctgttgcttttcaatttgctataatacttatcctgatcacaactcaaatttcatggtag
||||| |||||||| || || ||| | |||||||||||||| ||||||||||||||||| || |||||||  | |||     ||   || |||         |    |  |    ||||||| || ||| | | ||     | | | |||| ||||| ||| |||
ATGGGCAAGGATGTCGTTTCGTTCTTGTCATGGGCAGCTGAACCTGAGATGGAAGAGAGGAAACTGgtaatcagctcaacttttgtccattta---------tatattact----ttcaattcgcaatatttcctaataccaac-ctactctaatttgatg-tag

upper sequence: GRMZM2G032367_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcgcgacttaatcaattaactgcagtttg-cgctgttgcttttcaatttgctataatacttatcctgatcacaactcaaatttcatggtag
|||||||| ||| |||||||||||||  | ||||| || || |||||||||||||||||||| |||||       ||     |||  |  ||  |  ||| |       |    | || | |||   |  | | |  | |      ||                  
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgt--ttgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaaggacattgctaccatatgcag-----------------

upper sequence: GRMZM2G032367_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 7
ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcgcgacttaatcaattaactgcagtttg-cgctgttgcttttcaatttgctata-atacttatcctgatcacaactcaaatttcatggtag
|||||||| ||  |||||||||||||  | ||||| || || |||||||||||||||||||| |||||       ||     |||  |  ||  |  ||| |       |    |  |  |||| |||   | | |  | |      ||                  
ATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgt--ttgtttcctttattatcctttttccaccagatcaataaagaaaatactttattttctaaggacattgctgccatatgcag-----------------

upper sequence: GRMZM2G032367_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 7
ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaa---caacctcgcgacttaatcaattaac--tgcagtttgcgctgttgcttttcaatttgctataatacttatcctgatcacaactcaaatttcatggtag
|||||||| ||| ||||||||||| |  | ||||||||||| || || ||||||||||| || ||||||     | | |      ||      | |||  || | |||   |     || | |||||   ||  | | |||   | || |    |||| ||   |  |||
ATGGGTAAAGATATTGTATCATTCTTGGCCTGGGCAGCTGAACCAGAAATGGAAGAGAGGAAACTGgtaggtttatctttctctgttcgctggtgaacattgtattttctccctagactatgcaatt-aatactagatttagttt-atgatcgatcaagttgact--tag

upper sequence: GRMZM2G032367_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 6
ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcgcgacttaatcaattaactgcagtttgcgctgttgcttttcaatttgc-----tataatacttatcctgatcacaactcaaatttcatggtag
|||||||| ||||||||||| ||| | || ||||||||||| || |||||||||||||| ||  |||||  |   ||     || ||  |||  |     |||  ||||| | ||    || | |     |  ||||   ||    |||   | ||  |||   || |  
ATGGGTAAAGATGTTGTATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTGgta--agtttcttagtttcatatatt--ccatgttttaagctgtcgtttccatatgtacgagattgcaataggaatatcaatctggattctgattatttgattt

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|4885946|gb|AI677066.1|AI677066
EST:     CCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: CCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|71763205|gb|DR961142.1|DR961142
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|5006059|gb|AI712121.1|AI712121
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAAAGAAAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCCCTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|14245130|gb|BG873712.1|BG873712
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|76290228|gb|DV029796.1|DV029796
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTTTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|32938109|gb|CF042928.1|CF042928
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTCCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|71757789|gb|DR955726.1|DR955726
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTTTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|5608164|gb|AI901831.1|AI901831
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|211323657|gb|FL286663.1|FL286663
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTCCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|37386374|gb|CF630373.1|CF630373
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTCCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|37419011|gb|CF647179.1|CF647179
EST:     GAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: GAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|32939220|gb|CF044039.1|CF044039
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTCCTACTATCACTGGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|29947382|gb|CB816627.1|CB816627
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|37419478|gb|CF647422.1|CF647422
EST:     GAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: GAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
EST: gi|78026464|gb|DV494851.1|DV494851
EST:     TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG                         ATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA
genomic: TATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCA

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: 89

ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCATACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGTAAGCTGGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCATACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGTAAGCTGGTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCATACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGTAAGCTGGTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 167

ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacct ... ttcatggtagATGGGAGTGAAATGGATCTTTCTACTATCACTAGCGCTTCTTCAAGCTGCATACTACCGCCGCATGAGGTGGTCAGTCTTGAAGTCCCGTAAGCTGGTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcgcgacttaatcaattaactgcagtttgcgctgttgcttttcaatttgctataatacttatcctgatcacaactcaaatttcatggtag

- - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG