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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG

Basic information

species Zea mays
transcript GRMZM5G824944_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 4
----tcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacc--cctcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG---------
     | || |||    ||| | | |     | |    |     |  | ||| ||||||   ||||  |||| |||   | |||   ||||| |||||||||||||| ||||| ||||||||||| ||||| | |||||| || ||||||||||| || ||||||||||| || ||||| || ||||||||||         
atgaacatgctgtgggaatggcat-tagacagatacactgaacacata-acattctgctttattctgctgactgactgacttccgtgcaggcggagaagcagATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCGAAAACTCAGTACTCGTTTTCGCATGTTCCATCCATGAAGGGCGCGCCGT

upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g27420.1 (Oryza sativa), 3'ss of exon 4
----------------tcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacc--cctcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG
                 | || |||    ||| | | |     | |    |     |  | ||| ||||||   ||||  |||| |||   | |||   ||||| |||||||||||||| ||||| ||||||||||| ||||| | |||||| || ||||||||||| || ||||||||||| || ||||| || |||||||   
cttttgacactgatgaacatgctgtgggaatggcat-tagacagatacactgaacacata-acattctgctttattctgctgactgactgacttccgtgcagGCGGAGAAGCAGATTGAAATGTATACCAAGCAAGGCTTCTCAAACCTCCCAATATGCATGGCGAAAACTCAGTACTCGTTTTCGCATGTTCCATCCATGA---

upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 4
-----------tcttgttgtaaccatgccgtgtgtgttg-gtctttttggtcctcatacactctgctgacttctcttgaccgacccc----tcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG
           | |  |||| |     |    |     | |  |||||  |  | || ||| ||     |  || ||   |   |      ||  | |||||||||||||||||||||||||| | ||||||||| || ||  | || || || |||||||| ||||| ||||| || |||||| |     |  |    |   
ataaaagtgcatataattgttatttaactaaatacaaagagattttttctttttgatgcaccctatgaccacctgtttggcattcttgttgtctaaccagGCTGAGAAGCAGATTGAGATGTATAGCAAGCAAGGATTTTCAGGTCTTCCAATATGCATGGCTAAGACTCAGTATTCTTTCTCAGACAATGCTGCAGCAA---

upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G44010.1 (Glycine max), 3'ss of exon 4
-tcttgttg--taaccatgccgtgtgtgttggtctttttggtcctc------atacactctgctgacttctcttgaccgacccc-------tcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG
   |||||   |||  |    | |  | |   |||||||     |       |  ||| ||     |  | | || | | |          ||  | |||||||||||||||||||||||||| | ||||||||| || ||  | || || || |||||||| ||||| ||||| || |||||| |     |  |    |   
tatttgttaactaaatacaaagagattttctctcttttttactgtttaatggacgcaccctttgaccaccacctgtctggcattcttgttgtctaaccagGCTGAGAAGCAGATTGAGATGTATAGCAAGCAAGGATTTTCAGGTCTTCCAATCTGCATGGCTAAGACTCAGTATTCTTTCTCAGACAATGCTGCAGCAA---

upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 4
tcttgttg-taaccatgccgtgtgtgttggtctttttg----gtcctcatac--actctgctgacttctcttgaccgacccctcccaa-----------caggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG
  |  ||| |  | |  |||  |   |   | | ||||    ||  ||| |   |  ||| | |  |  |||  |      |     |           ||||| ||||| |||||||||||||||||  | ||||| ||||| |  || ||||| |||||| |||| || |||||||| ||||||||||   | || | ||   
-gtgattgattcctagaccgacttcttcaatttctttgcattgttgtcaaaagaaacctgtttatgtaacttatctattatcctgtgatatgtaaaatacagGCAGAGAAACAGATTGAGATGTACACACAACAAGGCTTCTCGAATCTTCCCATATGCATGTCGAAAACACAGTACTCATTCTCACATGATGCATCAAAGA---

upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 4
--tcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttct----cttgac-cgacccctccc---------aacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG
    || ||| || |      ||   | ||     ||||  | |  |  ||  | | || |  |     |||||  ||   ||| |         || |||||||||| ||||||||||||||||  |  |||||||| || |  || ||||| |||||||| |||||||||||||| || |||||   | | ||  |||   
ccattttttgcaatctcagtttgccagatgtcaaatttgaacttgctgaacagttcagaatgttgccatttgacatgaattctctcttttgtgtgaatagGCTGAGAAACAGATTGAGATGTACAGTAGACAAGGGTTTTCTAATCTGCCCATCTGCATGGCCAAGACCCAGTACTCATTTTCACACACCGCTTCTGTGA---

upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27738 (Selaginella moellendorffii), 3'ss of exon 4
tcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG
                    ||  | |  ||  |||| | |||  |   ||| || | ||       |||| |  | |  |||||| ||     |||| ||| | ||||| |  ||||| |||||    || |||||||||||||||||||| |||||||||||||| || |  || ||  | |   
--------------------gtaagctc-tccatttgcttctcg-atcttcttctcatttgctcgtcccgatcgttgctcacagGCAGAAGCAAAGATCGAGCTCTACACGAGACAAGGCTTCTCGCAACTTCCCATTTGCATGGCGAAGACGCAGTACTCGTTCTCGCACGATCCATCGCTCA---

upper sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ37206 (Selaginella moellendorffii), 3'ss of exon 5
tcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG
                    ||  | |  ||  |||| | |||  |   ||| || | ||        ||| |    |  |||||| ||     |||| ||| | |||||    ||||| |||||    || |||||||||||||||||||| |||||||||||||| || |  || ||  | |   
--------------------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|37398596|gb|CF636612.1|CF636612
EST:     AATTGCT-AGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|37374265|gb|CF623478.1|CF623478
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|67016604|gb|CO445353.1|CO445353
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|40335763|gb|CK369833.1|CK369833
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATTTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|213175324|gb|FM194467.1|FM194467
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|37387441|gb|CF630914.1|CF630914
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATTTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|67033495|gb|CO462244.1|CO462244
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|71427606|gb|DR808656.1|DR808656
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|211371831|gb|FL183018.1|FL183018
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT
EST: gi|32857153|gb|CD996834.1|CD996834
EST:     AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATACTCCGAGCAGGCT-                         GAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAC
genomic: AATTGCTAAGTTCTATGGTGCTAGTGGCGTTGAATATTCCGAGCAGG-TAtcttgttgta ... ccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG
                                       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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgttgtaaccatgccgtgtgtgttggtctttttggtcctcatacactctgctgacttctcttgaccgacccctcccaacaggctGAGAAGCAGATTGAGATGTACACCAAGCAAGGGTTCTCCAGCCTCCCCATTTGCATGGCGAAGACCCAGTACTCGTTCTCACATGTCCCGTCCATGAAGG

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