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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataatttgaagcgtttctttttttctaaaacaaagctctaatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG

Basic information

species Zea mays
transcript GRMZM2G056014_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056014_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g02940.1 (Oryza sativa), 3'ss of exon 1
gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataatttgaagcgtttctttttttctaaaacaaagctctaatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG
                                             ||   | |  ||| | |||    | || |||||| |   |  | ||  | || |       |   |   ||  | ||| |   |    |||  |||| |||||||| |||||||| |||||||||||  | ||||| ||||||||||| ||||| ||| | ||||| ||||||||||| || || ||||||||||||||||
----------------------------------------ttagagataacatgaatttatagg----tcttttattgtcccaaaagtactgatatc-tgtgacataatttgaattggtatctcacttatttttcttttgtt-cagGTTGCAAAAGAGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAG

upper sequence: GRMZM2G056014_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataatttgaagcgtttctttttttctaaaac----aaagctct---aatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG
                                                                        ||| |  | ||      |  || | | |    |    | || |   | | | |       ||||||||   ||| |||||||| || || ||||| |||||| |||||||||| || || ||||| |||||||| ||| | || || |||||||| || || ||||| ||||||||||| |
------------------------------------------------------------------------gtagttgtttctcttctcccttctgaaaggacgggatgattatagctctatcagctttctaaagctcttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG

upper sequence: GRMZM2G056014_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G07810.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataat--ttgaagcgtttctttttttctaaaacaaagctctaatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG
                                                                   ||| ||| |   |   | | |  |   |||   ||  |   |||  |      |||||||| |   |  |  || || ||||| || || ||||| ||||||||||| ||||| || || ||||| |||||||| ||| | || || |||||||| || || ||||| ||||||||||| |
-------------------------------------------------------------------gtactgtttctcttctctcatcttcaattccggatgatgatagctctatcagctttctaaagctctgggc--attttgcagGTAGCAAAGGAGGCATCTGACATGGTTTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTAGGTGAAGGCAGGTCCATCTATAACAACATGAAGG

upper sequence: GRMZM2G056014_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g03900.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataatttgaagcgtttctttttttctaaaacaaagctctaatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG
                               |||  | | ||||       |||  |   | |  ||      ||||     | |  |  | ||||| || |    |  |||| |  ||||||||  |  |  |  | || || ||||||| || || || ||||||||||| ||||| || || ||||||| ||| |||||| |||| || |||||||| ||||| || |||||||| ||||| |
-------------------------------aatctagtcccca-----attttggtatgatgaagt------tattcaaaacta--tattcttttcttagtcc--attgtttatcgttttctaacccctatgtgcactgatttagGTTGCAAAGGAAGCCTCTGACATGGTCTTGGCAGATGATAATTTTAACACAATAGTTGCTGCTGTTGGTGAAGGCAGATCCATTTACAACAATATGAAGG

upper sequence: GRMZM2G056014_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0040g02830.t01 (Vitis vinifera), 3'ss of exon 5
gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataatttgaagcgtttctttttttctaaaacaaagctctaatgttt--cagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG
                                                   || | |||       |  |||  | |  | ||   |  | | ||| ||   ||   | |||| |   ||   | |   ||  |||  | |||  |||||||| ||||| || ||||| ||||||||||| ||||| |||||||| || |||||| |||| || || |||||  |||| ||||||||||| ||||| |
------------------------------------------------aaattatgttgctttctttacatttgagttgtttctgtcctcatatttaatgtcttactgtgtttatacattaaaatatttaatatcttctctttttcagGTTGCTAAAGAAGCCTCTGATATGGTGTTGGCAGACGATAATTTTAGTACAATAGTTGCTGCTGTTGGGGAAGGGCGATCTATCTACAACAATATGAAGG

upper sequence: GRMZM2G056014_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S80_36V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataatttgaagcgtttctttttttctaaaacaaagctctaatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG
                                          |||        |  || |        || |||  |||     ||     || | | | | ||  ||    |     |||  |      |||| || |  | |||||||||||||| ||  ||||||||||| |||| ||||||||||| ||||| || ||  | || || || || ||  |  | || ||||||||||||||||
-----------------------------------------gcacagtgatgatctttaacgttcaaataatgttctgtga---actcaaattctacttcaatt--agtacattgaaatttaaacttgtgagctgtacttgtgcagGTTGCCAAAGAAGCTGCTGACATGGTGCTGGCAGACGACAATTTCAGCACAATCGTGGCAGCTGTTGGAGAGGGTCGTGCAATTTACAACAACATGAAAG

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|31910148|gb|CD651279.1|CD651279
EST:     CTTTGAAGCTGGCTGACATCGGTGTAGCTATGGGCATTACTGGAACTGAG                         GTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACC
genomic: CTTTGAAGCTGGCTGACATCGGTGTAGCTATGGGCATTACTGGAACTGAGgtaaattcct ... aatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACC
EST: gi|211330037|gb|FL163566.1|FL163566
EST:     CTTTGAAGCTGGCTGACATCGGTGTAGCTATGGGCATTACTGGAACTGAG                         GTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACC
genomic: CTTTGAAGCTGGCTGACATCGGTGTAGCTATGGGCATTACTGGAACTGAGgtaaattcct ... aatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACC

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: 48

AGATGGGGAAGTTGTCGCCATGACTGGAGATGGAGTCAATGATGCCCCTGCTTTGAAGCTGGCTGACATCGGTGTAGCTATGGGCATTACTGGAACTGAGgtaaattcct ... aatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 92

AGATGGGGAAGTTGTCGCCATGACTGGAGATGGAGTCAATGATGCCCCTGCTTTGAAGCTGGCTGACATCGGTGTAGCTATGGGCATTACTGGAACTGAGgtaaattcct ... aatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 178

AGATGGGGAAGTTGTCGCCATGACTGGAGATGGAGTCAATGATGCCCCTGCTTTGAAGCTGGCTGACATCGGTGTAGCTATGGGCATTACTGGAACTGAGgtaaattcct ... aatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 240

AGATGGGGAAGTTGTCGCCATGACTGGAGATGGAGTCAATGATGCCCCTGCTTTGAAGCTGGCTGACATCGGTGTAGCTATGGGCATTACTGGAACTGAGgtaaattcct ... aatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcataatttgaagcgtttctttttttctaaaacaaagctctaatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG
                   tttctttttttctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattcctaccttctttctagttacctggaattcaatgcccacgactgcttttattgaaaggggtgtattgtattgttctccacctgcttttttcataatttgaagcgtttctttttttctaaaacaaagctctaatgtttcagGTTGCCAAAGAGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA