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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

Basic information

species Zea mays
transcript GRMZM2G064023_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g10070.2 (Oryza sativa), 3'ss of exon 1
--catttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
     | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagcagCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG

upper sequence: GRMZM2G064023_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 1
-----catttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
        | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
gcgcgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagCAGCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG

upper sequence: GRMZM2G064023_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
catttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTC-----CGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
  |  ||   || | |    | |    |  ||   |||   ||   |  | |  |||   || |  |   ||  | ||    ||     | |||| |     || ||  |    || |||     | |       |||| |||||||||||||||||||| |||||||| |||||| | ||||||||||||
-gtgagcgcgccctcgaactcgccttaaccttgtcttatcctccact-cgatctggaatggaagctaggttcaatctggggagtata-atatctgggggttggttcaattcaactgttaggtccacccctgcagGCGGCGATGGCGTTCTTCCGGGGCCTGACCGCGGTTTCGAGGATTCGATCCCGCATG

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|211269893|gb|FL099813.1|FL099813
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269901|gb|FL099821.1|FL099821
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGYGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT-                         --GTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269898|gb|FL099818.1|FL099818
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269895|gb|FL099815.1|FL099815
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|8103179|gb|AW927835.1|AW927835
EST:     CGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGG-GGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: CGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269899|gb|FL099819.1|FL099819
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211399064|gb|FL099823.1|FL099823
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269896|gb|FL099816.1|FL099816
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269891|gb|FL099811.1|FL099811
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269897|gb|FL099817.1|FL099817
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269889|gb|FL099809.1|FL099809
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|148967125|gb|EE018300.2|EE018300
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269900|gb|FL099820.1|FL099820
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269890|gb|FL099810.1|FL099810
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211399065|gb|FL099824.1|FL099824
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269892|gb|FL099812.1|FL099812
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|76287895|gb|DV027463.1|DV027463
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT-                         --GTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211399063|gb|FL099822.1|FL099822
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|211269894|gb|FL099814.1|FL099814
EST:     CGCGCCCCGTCCTCGCCCGGCCGGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: CGCGCCCCGTCCTCGCCC-GCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|149090362|gb|EE179668.2|EE179668
EST:     CGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT-                         --GTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: CGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|149077813|gb|EE166538.2|EE166538
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     CGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG
genomic: CGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGG

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), 47 (downstream exon)
Score: 64

ATTCATGTCCCGAGAACTTGTCAGGCTCTCTTCCTCCCTCGCCGCGGAACACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 81

ATTCATGTCCCGAGAACTTGTCAGGCTCTCTTCCTCCCTCGCCGCGGAACACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

ATTCATGTCCCGAGAACTTGTCAGGCTCTCTTCCTCCCTCGCCGCGGAACACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 102

ATTCATGTCCCGAGAACTTGTCAGGCTCTCTTCCTCCCTCGCCGCGGAACACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... gtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
                             tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagCAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

- - tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcctg