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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatacttcaccactgaaagaacaaatacattttttttctgctgcttttatttttatataattgctgctgttgtgtgtatgaacataccatatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAA

Basic information

species Zea mays
transcript GRMZM2G063851_T04
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 14
------------------------------gcatacttcacc--actgaaa--gaacaaatacattttttt---tctgctgctt-ttatttttatataattgctgctgttgtgtgta-tgaacatac----catatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAA
                              |  | |  || |   || |||  ||   | | |  | ||     | ||||||   | ||||||| ||   |  |    ||||||| | ||| ||||     ||| || ||||||||||||| || ||||||||||||||||| |  || || || |||| |||||| || |||||||||||||| ||||| |||||||||||||| |||||||
gtatatgctcagtttgttgcactggatcttgtttgccgcatcctgctaaaaaggactcattgcgctattcaacatatgctgcagatcatttttaaatcgatttttagtttgtgtgaactgaccatagtcaacatgtaatgcagGAAGTGCTGTTGTGGATCAAATCTGTAATAGGTGAGACAGGTAGTGATGTTACAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAA

upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 14
---------------------------------------------------------------------------------gcatacttcaccactgaaagaacaaatacattttttttctgctgcttttatttttatataattgctgctgttgtgtgta-tgaacatac----catatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAA
                                                                                  |  |  | | |  || |||||  || | | | ||  |   |   |||||  || ||||  ||  ||    |||||| | | | ||||     |||  | ||||||||||| | || ||||||||||||||||| |  || ||||| ||||  ||||| || |||||||||||||| ||||| |||||||||||||| |||||||
gtatgctcagtttgttgtactggatcttctctgccacatcctgctaaacaaggattcactgcattgcatactcaaaatatgtcgcagattatctttggaagaaggaacataatgttcctt--ccatttttaaattgatatt-ttagtgtgtgtgtgtgaactaaccatagttcacatccaatgcagGAAGTGTTGTTGTGGATCAAATCTGTAATAGGTGAGACTGGTAGTGACGTTACAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAA
















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|116813560|gb|EC856011.1|EC856011
EST:     CAGCGGC-CTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
genomic: CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
EST: gi|78179069|gb|DV549442.1|DV549442
EST:     CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
genomic: CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
EST: gi|31364242|gb|CD448597.1|CD448597
EST:     CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
genomic: CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
EST: gi|76010584|gb|DT937754.1|DT937754
EST:     CATGGCCTTGCAAATCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
genomic: CATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
EST: gi|6964715|gb|AW433408.1|AW433408
EST:     CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
genomic: CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
EST: gi|76010585|gb|DT937755.1|DT937755
EST:     CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
genomic: CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
EST: gi|7145414|gb|AW506895.1|AW506895
EST:     CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGAGAGTGGTGTT
genomic: CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     CAGCGGCTCTTAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAA-TCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTG
genomic: CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTG
EST: gi|116825307|gb|EC869024.1|EC869024
EST:     CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG                         GAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGCGGTGTT
genomic: CAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAGgtgtgttcag ... tatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatttttatataattgctgctgttgtgtgtatgaacataccatatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAA
     tttttatataattgct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatacttcaccactgaaagaacaaatacattttttttctgctgcttttatttttatataattgctgctgttgtgtgtatgaacataccatatattgcagGAAGTGCTTTTATGGATCAAATCTGTAATTGAGGAAACTGGGAGTGGTGTTACCACAGATCAACTCAAAGACTATGTCTGGAAGACACTAAAGAGTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA