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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcatctgctatcaaatcgtgtcatgaaatcactggtggtactttgtaggctgaatgttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG

Basic information

species Zea mays
transcript GRMZM2G131853_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
gtttgcatctgctatcaaatcgtgtcatgaaatcactggtggtactttgtaggctgaat-gttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
||||  |||| || |||     |    |  |  || |  |     | ||| | ||||    ||| || || | |||  | ||   ||||||||||||| ||||| ||||| || |||||||||||||||||||| ||||| |||||||| ||||||||||||||||| |||||||||||||||
gtttctatctcctgtca-----tccattagagacagtaatttaggtctgtggactgatccatttcttgtttttttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG

upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G08320.1 (Glycine max), 3'ss of exon 9
-------------------gtttgcat-ctgctatcaaatcgtgtcatgaaatca--ct------ggtggtactttgtaggctgaatgttttt-tcttctctttcttcatcca-------agATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
                    | || || ||| |  |   |  ||   |   ||||  ||       || ||  | |||   || | |  ||   |||   ||||  | ||  |       || | ||||| || || || ||||| || || ||||||||||||||||| ||    ||||| ||||| |||||||| ||||| || ||||||||||||
gtacattttttttgtgttcttctgtatactgttcccttgttttgctttatgatcagactttccaaagttgtgttctgtctacttatttcttcaatctgagcttttattatgtacttctatagGTCTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATTAAAGCTCACCCATGGCACAAG

upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 9
-------gtttgcatctgctatcaaatcgtgtcatgaaatcactg---gtggtactttgtaggctgaatgttttttcttct-----------ctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG-
         |||  |    ||||     || | || |  |   ||   || | |   | | || ||    || |    |||            | | | ||    |||| ||||| || || || ||||| || || | ||||||||||||||||||  ||||||| ||||| |||||||||||||| || |||||||| ||| 
taaagttaattgtgttctttatccttgtgttttataagcttcttgaaagttgcatcctattggttgtggattatagaatctgagtgtaattattatgtgcactatagaTCTTGGGAACACCGACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAGG

upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 9
--------------------------gtttgcatctgctatcaaatcgtg-tcatgaaatcactggtggtactttgtaggctgaatgttttt-tcttctctttcttcatcca-------agATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
                            |  |  ||  | | |  |  || ||||    ||    || ||  |  ||  ||| | |  ||   |||   ||||| | ||  |       |||||||||| || || || ||||| || || ||||||||||||||||| ||    ||||| ||||| |||||||| ||||| || ||||||||||||
gtacattttcatgtgttcttcagaatactgtccccttgttttactttatgatcatactttccaaagttgtgttcggtctgcttatttcttcaatctgagctttcattatgtacttctatagATTTTGGGAACACCCACCAGAGAAGAAATAAGGTGCATGAATCCAAACTACAATGAATTTAAGTTTCCTCAGATCAAAGCTCACCCATGGCACAAG

upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
--------gtttgcatctgctatcaaatcgtgtcatgaaatcactg---gtggtactttgtaggctgaatgttttttcttct--------ctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
          |||  |    ||||     |  | || |  |   ||   || | |   ||| || |     |  ||   |||         | | | ||    |||| ||||| || ||||| ||||| || || | ||||||||||||||||||  ||||||| ||||| |||||||||||||| || |||||||| |||
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG

upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtttgcatctgctatcaaatcgtgtcatgaaatcactggtggtactttgtaggctgaatgttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
       |  || ||  | || ||   |    |  ||| |  |  ||||   |  |     ||  ||    ||| |||   |  || | || |||||||| ||  | ||||| ||||  |||||||||||||| ||  | || || |||||||||||||| ||||| ||||| |||||||||
------gtacgc-atgcattcttgctcttttttttctgtt--ttttttgcgagtcg--ctcttgctcaagacttgcttttgc--agGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtttgcatctgctatcaaatcgtgt-catgaaatc--actggtggtactttgtaggctgaatgttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
                     ||   |||| | ||   ||     |  | | |  ||     | | || ||      |     |   || | || |||||||| ||  | ||||| ||||  |||||||||||||| ||  | || || |||||||||||||| ||||| ||||| |||||||||
---------------------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttgcttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 8
gtttgcatctgctatcaaatcgtgtcatgaaatcactggtggtactttgtag--gctgaatgttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
                           |    ||  || |  | | || | |  ||||   | |  |     |     |       || || | || || || ||  | |||||||||| ||| |||||||| || ||  | ||||||||||||||||| || || ||||| || |||||||||
--------------------------gttggctcgttgtttttgccttatggtggctgggcgctcataaagttggacttgggc---agGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCACCCTTGGCACAAG

upper sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 8
gtttgcatctgctatcaaatcgtgtcatgaaatcactggtggtactttgtag--gctgaatgttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
                           |    ||  || |  | | || | |  ||||   | |  |     |     | |     || || | || || || ||  | |||||||||| ||| |||||||| || ||  | ||||||||||||||||| || || |||||||| |||||||||
--------------------------gttggctcgttgtttttgccttatggtggctgggcgctcataaagttggacttgcgc---agGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG

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|211457391|gb|FL214355.1|FL214355
EST:     CTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAG                         ATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTAT
genomic: CTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAGgtttgcatct ... ttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTAT
EST: gi|211457390|gb|FL214354.1|FL214354
EST:     CTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAG                         ATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTAT
genomic: CTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAGgtttgcatct ... ttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTAT

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), 45 (downstream exon)
Score: 277

CCTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAGgtttgcatct ... ttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 22

CCTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAGgtttgcatct ... ttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 61

CCTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAGgtttgcatct ... ttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 58

CCTTTGTTTCCTGGTGAAAGTGGTGTTGACCAACTGGTGGAAATAATAAAGgtttgcatct ... ttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcactggtggtactttgtaggctgaatgttttttcttctctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG
                           tgttttttcttctctt  CT-rich tract
                         aatgtttttt  TA-rich tract