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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagtatgttctacatctactccactcacgttgcccggcattgcctcggtaattcgtctgtgtgatgtgagtcacgtgtcgtctgtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG

Basic information

species Zea mays
transcript GRMZM2G162284_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162284_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g37910.3 (Oryza sativa), 3'ss of exon 5
gtgcagtatgttctacatctactccactcacgttgcccggcattgcctcggtaattcgtctgtgtgatgtgagtcacgtgtcgtctgtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG---
        |  ||  | ||| | | ||||      || |  | || |  |  |  | |    ||   |||       ||| ||| | ||  ||||| |   |||||| ||  |    || || || ||||||||||||||||||||||| ||||||| ||||||||     
-------gtaatccccctctccacaactctg--cacctgcaactgtcatgacacattgaaactgatctgt------tgtg-cgtttctcgttgcagGC---AGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGGCAGC

upper sequence: GRMZM2G162284_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g37910.1 (Oryza sativa), 3'ss of exon 6
gtgcagtatgttctacatctactccactcacgttgcccggcattgcctcggtaattcgtctgtgtgatgtgagtcacgtgtcgtctgtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG-------------------------------
        |  ||  | ||| | | ||||      || |  | || |  |  |  | |    ||   |||       ||| ||| | ||  ||||| |   |||||| ||  |    || || || ||||||||||||||||||||||| ||||||| ||||||||                                 
-------gtaatccccctctccacaactctg--cacctgcaactgtcatgacacattgaaactgatctgt------tgtg-cgtttctcgttgcagGC---AGGAGGCCCGGCTACCTCAGGCGACTCTGACAAGTCCAAGTCCGAGGTGAACGACGAGGACGAGGGCAGCGTAAGACCTCCCTCCAATCCGCAACACC
















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|22472639|gb|BU037119.1|BU037119
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|67041980|gb|CO468235.1|CO468235
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCT---GGAGGACCCACAGAGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|31359518|gb|CD443875.1|CD443875
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|67015235|gb|CO443984.1|CO443984
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCT---GGAGGACCCACAGAGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|211010350|gb|FL233636.1|FL233636
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCYATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGA
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGA
EST: gi|14203924|gb|BG837601.1|BG837601
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|26558436|gb|CA830671.1|CA830671
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|21891488|gb|BQ744701.1|BQ744701
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|211010348|gb|FL233634.1|FL233634
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|28984233|gb|BQ539002.2|BQ539002
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|71436984|gb|DR818034.1|DR818034
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|211010351|gb|FL233637.1|FL233637
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|211010356|gb|FL233642.1|FL233642
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|4874486|gb|AI674006.1|AI674006
EST:     AGCTGAAGGTTGAGTACNCAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCCCATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|78112438|gb|DV530832.1|DV530832
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|211159313|gb|FL469871.1|FL469871
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TYTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|87155374|gb|DY400163.1|DY400163
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
EST: gi|21828650|gb|BQ703334.1|BQ703334
EST:     AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAG                         TCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG
genomic: AGCTGAAGGTTGAGTACACAAAGAAGATGGACGCCTATAACAACAAGCAGgtgcagtatg ... gtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcctcggtaattcgtctgtgtgatgtgagtcacgtgtcgtctgtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG
          taatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcagtatgttctacatctactccactcacgttgcccggcattgcctcggtaattcgtctgtgtgatgtgagtcacgtgtcgtctgtcactgcagTCTGGAGGAGGACCCACATTGTCTGGTGATTCTGACAAGTCCAAGTCCGAGGTCAACGACGGGGACGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG