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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttgcatctttaattcatagatttgtttttttccccatccattccttgcaagccctacactaaaaatggatggctgtgtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGTACTACTGTACGCAGCACAAAGAAGACATTTTGGCAATGTTGCAGCGTTG

Basic information

species Zea mays
transcript GRMZM2G011364_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011364_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g39650.1 (Oryza sativa), 3'ss of exon 9
gtacgttgcatctttaattcatagatttgtttttttccccatccattccttgcaagccctacactaaaaatggatggctgtgtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGTACTACTGTACGCAGCACAAAGAAGACATTTTGGCAATGTTGCAGCGTTG
||| |   |||||||| ||  ||   |||||||||   |   ||| || | ||| | ||| |  |||| |||  || || ||| ||| |||| | ||| |||||| ||||| |||| ||| ||||||||||||||||||  ||||||| || |||||| ||||| ||  | || |||| ||| |  | |||
gtatgccacatctttatttgtta---ttgttttttatacttgccagtcgt-gcatgtcctcc--taaatatgtttg-ctttgttctggcagGTATAAGTATATGGACCATGATACTGGTTATTATTCTTGCAATTTTGGCATACTACTATATGCAGCATAAAGAGGATCTCTTAGCAAGGTTTCTACATTG
















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|86469466|gb|DY235836.1|DY235836
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|71434095|gb|DR815145.1|DR815145
EST:     TTCGACTCTTCTGCAAGGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: TTCGACTCTTCTGCAA-GGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|148957846|gb|EC903996.2|EC903996
EST:     CTTCGACTTTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|86473129|gb|DY239499.1|DY239499
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|5871274|gb|AW017745.1|AW017745
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|211396348|gb|FL437335.1|FL437335
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|78081363|gb|DV509775.1|DV509775
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|84977010|gb|DW475432.1|DW475432
EST:     CTACGACTCTTCCGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|149096645|gb|EE182410.2|EE182410
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|32945451|gb|CF050270.1|CF050270
EST:     CTTCGACTATAATGCAAGGGTGACATCTGTTGGGTCCCCAAAGAGTAATG                         GAACAACCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|6020933|gb|AW065861.1|AW065861
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGATATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|78083928|gb|DV512321.1|DV512321
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|149070572|gb|EE158978.2|EE158978
EST:     CTTCGACTTTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|78021573|gb|DV489960.1|DV489960
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|71595876|gb|DR906627.1|DR906627
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
EST: gi|110219160|gb|EC901058.1|EC901058
EST:     CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATG                         GAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT
genomic: CTTCGACTCTTCTGCAAGGGTGACATCTGTTGGGTCTCCAAAGAGTAATGgtacgttgca ... gtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccatccattccttgcaagccctacactaaaaatggatggctgtgtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGTACTACTGTACGCAGCACAAAGAAGACATTTTGGCAATGTTGCAGCGTTG
                         cactaaa  putative branch site (score: 2)
                          actaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttgcatctttaattcatagatttgtttttttccccatccattccttgcaagccctacactaaaaatggatggctgtgtcctgacagGAACAAGCATATGGCCCATGCTACTAGTTGTTATTCTTGCAATTTTGGTGTACTACTGTACGCAGCACAAAGAAGACATTTTGGCAATGTTGCAGCGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG