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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagtctctgaaagaaatacatttttcctgctgctgctcatatttttctgtactcgctattgttgggtgtatgaactatgaactcaccttatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTTACGACAGACCAACTCAAAGACTATGTCTGGAAGACACTGAAGAGTGGAA

Basic information

species Zea mays
transcript GRMZM2G063909_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 14
--------------------------------------------------------------------------------------tcaagtctctgaaagaaatacatttttcctgctgctgctcatatttttctgtactcgctattgttgggtgtatgaactatgaactcaccttatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTTACGACAGACCAACTCAAAGACTATGTCTGGAAGACACTGAAGAGTGGAA
                                                                                           ||| || |||||  |   |  |  | || |   |  ||  ||  | |  | |    ||| | ||| |  ||| || |  |||| |   | ||||||||| | |  | ||| |||| ||| ||||    || || || || |||||||| || || ||||||||||| ||||| ||||||||||| || |||||||
gtatgctcagtttgttgtactggatcttctctgccacatcctgctaaacaaggattcactgcattgcatactcaaaatatgtcgcagattatctttggaagaaggaacataatgttccttccatttttaaattgatattttagtgtgtgt-gtgtgaactaaccat-agttcacatc-caatgcagGAAGTGTTGTTGTGGATCAAATCTGTAATAGGTGAGACTGGTAGTGACGTTACAACTGATCAACTCAAAGAGTATGTGTGGAAGACACTAAAAAGTGGAA
















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|211458206|gb|FL358448.1|FL358448
EST:     CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAA                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
EST: gi|60345083|gb|DN212056.1|DN212056
EST:     CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
EST: gi|40334210|gb|CK368280.1|CK368280
EST:     CATCATCTGTGAATGGGTT-GCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
EST: gi|60400601|gb|DN233408.1|DN233408
EST:     CCACTACATGGCCTTGCAAATCAG                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
EST: gi|60354991|gb|DN221964.1|DN221964
EST:     CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG                         GAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT
genomic: CATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAGgtatgctcag ... tatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtactcgctattgttgggtgtatgaactatgaactcaccttatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTTACGACAGACCAACTCAAAGACTATGTCTGGAAGACACTGAAGAGTGGAA
                                    aactcac  putative branch site (score: 2)
                                      ctcacctt  CT-rich tract
                                            ttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaagtctctgaaagaaatacatttttcctgctgctgctcatatttttctgtactcgctattgttgggtgtatgaactatgaactcaccttatattgcagGAAGCGCTTCTATGGCTCAAGTCTATAATTCAGGAAACAGGGAGCGACGTTACGACAGACCAACTCAAAGACTATGTCTGGAAGACACTGAAGAGTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - -aaagaaa
- - - - - - - - - tacattt
- - - - - - - - - - - - - - - gctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtatg