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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA

Basic information

species Zea mays
transcript GRMZM5G824944_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 4
-gtatcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacc--cctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA------------
   | | || |||    ||| | | |     | |    |     |  | ||| ||||||   ||||  |||| |||   | |||   ||||| |||||||||||||| ||||| ||||||||||| ||||| | |||||| || ||||||||||| || ||||||||||| || ||||| || |||||||            
atgaacatgctgtgggaatggcat-tagacagatacactgaacacata-acattctgctttattctgctgactgactgacttccgtgcaggcggagaagcagATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCGAAAACTCAGTACTCGTTTTCGCATGTTCCATCCATGAAGGGCGCGCCGT

upper sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g27420.1 (Oryza sativa), 3'ss of exon 4
-------------gtatcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacc--cctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA
               | | || |||    ||| | | |     | |    |     |  | ||| ||||||   ||||  |||| |||   | |||   ||||| |||||||||||||| ||||| ||||||||||| ||||| | |||||| || ||||||||||| || ||||||||||| || ||||| || |||||||
cttttgacactgatgaacatgctgtgggaatggcat-tagacagatacactgaacacata-acattctgctttattctgctgactgactgacttccgtgcagGCGGAGAAGCAGATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCGAAAACTCAGTACTCGTTTTCGCATGTTCCATCCATGA

upper sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 4
--------gtatcttgttgtaaccatgccgtgtgtgttg-gtctttttggtcctcatacactctgctgacttctcttgaccgacccc----tcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA
        | || |  |||| |     |    |     | |  |||||  |  | || ||| ||     |  || ||   |   |      ||  | |||||||||||||||||||||||||| | ||||||||| || ||  | || || || |||||||| ||||| ||||| || |||||| |     |  |    |
ataaaagtgcatataattgttatttaactaaatacaaagagattttttctttttgatgcaccctatgaccacctgtttggcattcttgttgtctaaccagGCTGAGAAGCAGATTGAGATGTATAGCAAGCAAGGATTTTCAGGTCTTCCAATATGCATGGCTAAGACTCAGTATTCTTTCTCAGACAATGCTGCAGCAA

upper sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G44010.1 (Glycine max), 3'ss of exon 4
------gtatcttgttgtaaccatgccgtgtgtgttggt--ctttttggtcctcatacactctgctgact-tctcttgaccgacccc----tcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA
       || ||   |  ||  |     | | | ||  |  || |||  |   |  || || ||   ||   || |    |   |      ||  | |||||||||||||||||||||||||| | ||||||||| || ||  | || || || |||||||| ||||| ||||| || |||||| |     |  |    |
tatttgttaactaaatacaaagagattttctctcttttttactgtttaatggacgcaccctttgaccaccacctgtctggcattcttgttgtctaaccagGCTGAGAAGCAGATTGAGATGTATAGCAAGCAAGGATTTTCAGGTCTTCCAATCTGCATGGCTAAGACTCAGTATTCTTTCTCAGACAATGCTGCAGCAA

upper sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatcttgttg-taaccatgccgtgtgtgttggtctttttggtcctcatac--actctgctgacttctcttgaccgacccctcccaa-----------cagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA
||   |  ||  ||  |   |    |   ||  | |   | ||  ||| |   |  ||| | |  |  |||  |      |     |           ||||| ||||| |||||||||||||||||  | ||||| ||||| |  || ||||| |||||| |||| || |||||||| ||||||||||   | || | ||
gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA

upper sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 4
--gtatcttgt--tgtaaccatgccgtgtgtg----ttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctccc-----aacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA
   | | |||   | | |   ||||   |||     |||  |||  ||  |     | | | |    | ||  | |||     | ||        || |||||||||| ||||||||||||||||  |  |||||||| || |  || ||||| |||||||| |||||||||||||| || |||||   | | ||  |||
ccattttttgcaatctcagtttgccagatgtcaaatttgaacttgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA

upper sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27738 (Selaginella moellendorffii), 3'ss of exon 4
gtatcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA
                       ||  | |  ||  |||| | |||  |   ||| || | ||       |||| |  | |  |||||| ||     |||| ||| | ||||| |  ||||| |||||    || |||||||||||||||||||| |||||||||||||| || |  || ||  | |
-----------------------gtaagctc-tccatttgcttctcg-atcttcttctcatttgctcgtcccgatcgttgctcacagGCAGAAGCAAAGATCGAGCTCTACACGAGACAAGGCTTCTCGCAACTTCCCATTTGCATGGCGAAGACGCAGTACTCGTTCTCGCACGATCCATCGCTCA

upper sequence: GRMZM5G824944_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ37206 (Selaginella moellendorffii), 3'ss of exon 5
gtatcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA
                       ||  | |  ||  |||| | |||  |   ||| || | ||        ||| |    |  |||||| ||     |||| ||| | |||||    ||||| |||||    || |||||||||||||||||||| |||||||||||||| || |  || ||  | |
-----------------------gtaagctc-tccatttgcttctcg-attttcttctcatttgctcgtctcgatcgtcgctcacagGCAGAAGCAAAGATCGAGCTCTACACGCGACAAGGCTTCTCGCAACTTCCCATTTGCATGGCGAAGACGCAGTACTCGTTCTCGCACGATCCATCGCTCA

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|166531724|gb|EG074046.1|EG074046
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGC
EST: gi|37374265|gb|CF623478.1|CF623478
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|37398596|gb|CF636612.1|CF636612
EST:     AGTCAATTGCT-AGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|67016604|gb|CO445353.1|CO445353
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|32857153|gb|CD996834.1|CD996834
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATACTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|213175324|gb|FM194467.1|FM194467
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|211371831|gb|FL183018.1|FL183018
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|37387441|gb|CF630914.1|CF630914
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATTTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|40335763|gb|CK369833.1|CK369833
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATTTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|71427606|gb|DR808656.1|DR808656
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
EST: gi|67033495|gb|CO462244.1|CO462244
EST:     AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAG                         GCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC
genomic: AGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCC

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: 155

ACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 460

ACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 539

ACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 279

ACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGTCAATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGgtatcttgtt ... ctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA
                                          cccctccc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacagGCTGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA