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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

Basic information

species Zea mays
transcript GRMZM2G064023_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g10070.2 (Oryza sativa), 3'ss of exon 1
-----ttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
     | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
cgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagcagCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG

upper sequence: GRMZM2G064023_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 1
--------ttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
        | |  |    |  |||  |   ||  ||| |||| | || ||      | | |   ||| |  ||||| |  ||  ||| ||     || || |||||||      |||  || |||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| ||
gcgcgtggtggtgtttaattatttttttgcgggattttggttgattttgggatgtattatgttctgacgaaatcgtttacttcgttgttt-----gtttgcgcagCAGCT----TGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG

upper sequence: GRMZM2G064023_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 1
--ttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTC-----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|211269895|gb|FL099815.1|FL099815
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211399063|gb|FL099822.1|FL099822
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|8103179|gb|AW927835.1|AW927835
EST:     CGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: CGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269896|gb|FL099816.1|FL099816
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|76287895|gb|DV027463.1|DV027463
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         TGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCC
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... tgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCC
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     CGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: CGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269899|gb|FL099819.1|FL099819
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269892|gb|FL099812.1|FL099812
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         TGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCC
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... tgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCC
EST: gi|211269897|gb|FL099817.1|FL099817
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269890|gb|FL099810.1|FL099810
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211399064|gb|FL099823.1|FL099823
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211399065|gb|FL099824.1|FL099824
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269891|gb|FL099811.1|FL099811
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269894|gb|FL099814.1|FL099814
EST:     CGCGCCCCGTCCTCGCCCGGCCGGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: CGCGCCCCGTCCTCGCCC-GCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269901|gb|FL099821.1|FL099821
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|148967125|gb|EE018300.2|EE018300
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269889|gb|FL099809.1|FL099809
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269900|gb|FL099820.1|FL099820
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269898|gb|FL099818.1|FL099818
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|149077813|gb|EE166538.2|EE166538
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|211269893|gb|FL099813.1|FL099813
EST:     ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGCAG                       
genomic: ACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTT---Ggtaagcaatt ... tgtgcagc
EST: gi|149090362|gb|EE179668.2|EE179668
EST:     CGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTG                         TGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCC
genomic: CGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... tgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCC

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), 35 (downstream exon)
Score: 9

ATTCATGTCCCGAGAACTTGTCAGGCTCTCTTCCTCCCTCGCCGCGGAACACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... tgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 23

ATTCATGTCCCGAGAACTTGTCAGGCTCTCTTCCTCCCTCGCCGCGGAACACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... tgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 15

ATTCATGTCCCGAGAACTTGTCAGGCTCTCTTCCTCCCTCGCCGCGGAACACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... tgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 39

ATTCATGTCCCGAGAACTTGTCAGGCTCTCTTCCTCCCTCGCCGCGGAACACGCGCCCCGTCCTCGCCCGCCCGTGTTCATCTCTCCATTCCATACCTTGgtaagcaatt ... tgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG
                          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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcttcccgtagtttcctctgggagtttcggttaaattcggttgtggtgaggacatgatgggatcgtctgtttgtttggttcctgtgtctgtgcagcagTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATG

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