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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactacatgatcaacatttatttttaaaaatattttttggtatatattaggatattgtcgactttttaatccatgtggttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACACAGGCTCTATGGAGGTACACATCTATCAGTGAATGGTGTTTCGTCAATGA

Basic information

species Zea mays
transcript GRMZM5G812553_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089860_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g03400.2 (Oryza sativa), 3'ss of exon 10
gtaactacatgatcaacatttatttttaaaaatattttttggtatatattaggatattgtcgacttt-ttaatccatgtggttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACACAGGCTCTATGGAGGTACACATCTATCAGTGAATGGTGTTTCGTCAATGA
||  ||| |   |||   ||| | ||||    || ||||  |||   |||| || |   | | |||| |||||  |||||    ||  ||||| |||||||||||||||||||||||| | || ||  | || ||||| || ||  | |||||||| || ||||||||||||| |||||| || || || |
gtgcctaaaaagtca---tttttcttta----tagttttgagtaagcattaagaaaagttagcctttgttaatttatgtgtcatttcatagGTCGTTATTCTTCAAGATTTCAAATGGCATGATTTCCTGCTCAAGCTTCATAGATTGTATGGAGGAACTCATCTATCAGTGACTGGTGTGTCATCGATAA

upper sequence: GRMZM2G089860_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv15s0046g01770.t01 (Vitis vinifera), 3'ss of exon 10
-------gtaactacatg--atcaacatttatttttaaaaatattttttggt--atatattaggata-----------ttgtcgactt----tttaatccatgtggtt--ctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACACAGGCTCTATGGAGGTACACATCTATCAGTGAATGGTGTTTCGTCAATGA
        |   | | ||  ||    | ||||| ||  |     ||||   |  | ||| |   |||           | ||| | ||    |||  | | |     |  || || ||||||| |||||||| || ||||||||||| ||||||||| | || ||||||| ||| ||    || |||||| | ||||| ||   ||| || ||||  |
gtagaacatttttccttggcattttgacttattcttctaccctcttttcatttaacataatgaaataagaagctttgctggtcaatttgagttttgcttcttactactatctctgcagGTTGTGATTCTTCAGGACTTCAAATGGTATGACTTTATTTTAAACCTACACAAGCTATACAAGGGGACACATTTGTCAGTAAAAAATGTATCTTCAAGAA
















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|60340406|gb|DN207379.1|DN207379
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|28873884|gb|CB329814.1|CB329814
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|37376011|gb|CF624501.1|CF624501
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|30032066|gb|CB833917.1|CB833917
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|32867364|gb|CF007046.1|CF007046
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|32933409|gb|CF038221.1|CF038221
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGT
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGT
EST: gi|148976018|gb|EE025877.2|EE025877
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|78105461|gb|DV523879.1|DV523879
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|50334433|gb|CO529559.1|CO529559
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|60339858|gb|DN206831.1|DN206831
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|91878206|gb|EB408163.1|EB408163
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|71436271|gb|DR817321.1|DR817321
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|60339048|gb|DN206021.1|DN206021
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|38687766|gb|CK144797.1|CK144797
EST:     GGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAAATGGTACGACTTTATTCTGAAGCTACA
genomic: GGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTC-AAATGGTACGACTTTATTCTGAAGCTACA
EST: gi|67022745|gb|CO451494.1|CO451494
EST:     GTGGTATGAAGATA-CTCCAACAGCTGATCCGTTTAGTGGCA-CCTTGAG                         GTTGT-ATTCTTC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTC
EST: gi|30307230|gb|CD001903.1|CD001903
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|29130015|gb|CB380719.1|CB380719
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|78121934|gb|DV540318.1|DV540318
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|60356994|gb|DN223967.1|DN223967
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|50334432|gb|CO529558.1|CO529558
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCACCCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|30087317|gb|CB885525.1|CB885525
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|76285903|gb|DV025471.1|DV025471
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|37382504|gb|CF628200.1|CF628200
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|116814031|gb|EC856531.1|EC856531
EST:     ACAGCTGAT-CGTTTAGTGGC-ACCTTGAG                         GTTGTTATTCTTCAAGA--TC-AATGGTACGACTTTATATCTGAAGCTACA
genomic: ACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTAT-TCTGAAGCTACA
EST: gi|211361286|gb|FL413661.1|FL413661
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|60355693|gb|DN222666.1|DN222666
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|50322459|gb|CO517585.1|CO517585
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|8102673|gb|AW927320.1|AW927320
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAA
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAA
EST: gi|60359029|gb|DN226002.1|DN226002
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|32867365|gb|CF007047.1|CF007047
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|31406360|gb|CD485092.1|CD485092
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|71764064|gb|DR962001.1|DR962001
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
EST: gi|67010879|gb|CO439628.1|CO439628
EST:     GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAG                         GTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC
genomic: GTGGTATGAAGATAACTCCAACAGCTGATCCGTTTAGTGGCAACCTTGAGgtaactacat ... ttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttggtatatattaggatattgtcgactttttaatccatgtggttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACACAGGCTCTATGGAGGTACACATCTATCAGTGAATGGTGTTTCGTCAATGA
                              ttttaat  putative branch site (score: 3)
                                             ttctttgt  putative PPT
       tatatattaggatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactacatgatcaacatttatttttaaaaatattttttggtatatattaggatattgtcgactttttaatccatgtggttctttgtagGTTGTTATTCTTCAAGATTTCAAATGGTACGACTTTATTCTGAAGCTACACAGGCTCTATGGAGGTACACATCTATCAGTGAATGGTGTTTCGTCAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG