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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgtttttaacaatgactatggttacatagttttaacaatgatttttttatagttttaacaataattatgcttacataagatattactaattagaaag...

Basic information

species Zea mays
transcript GRMZM2G029559_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029559_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 5'ss of exon 7
AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgtt-----tttaacaatgacta-tggttacatagttttaacaatgatttttttatagttttaacaataattatgcttacataagatat---tactaattagaaag
||||| ||||||||||| ||||| |||||  |||| ||||| || ||||||||| | || || ||||| ||||| |||||||||||||||||||| || |||| |||     |||   |   |||| |   || | |||||  | |  ||    ||||| |  ||         | || || || | |||||   ||| |||||| |  
AATCCTCTTGATTTGCTCCCTCCAAGCAAAATGATCCTTGATGAGTGGAAGAGGTTATACTCAAACACAAAAACAAACTTCCGTGAGGTTGCTATCAAGGgtaagtttcttttttggaatctactagtcagtaaaaagtttccagatagacaaatttattgcattg-------ctttg-ttgcaaaggatatgaatacaaattaggat-

upper sequence: GRMZM2G029559_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 5'ss of exon 6
AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgtttttaacaatgactatggttacatagttttaacaatgatttttttatagttttaacaataattatgcttacataagatattactaattagaaag----------
|| || ||||||||||| ||||| |||||| |||| ||||| || ||||||||| | || || ||||| ||||| || ||||||||||||||||| || |||| |||| |         | |||  |  ||||  | || |  |  |||  |       ||  ||| || |  ||    ||  || || | | || ||||          
AACCCTCTTGATTTGCTCCCTCCAAGCAAGATGATCCTTGATGAGTGGAAGAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct---------tttgggaatctagtagtcactaaaaggtttccacgtagaaaagtatagtt-tctttcgggaatctagtagtcactaaaaaggtttccacag

upper sequence: GRMZM2G029559_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT1G09640.1 (Arabidopsis thaliana), 5'ss of exon 7
AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgtttt--taacaatgacta--tggttacatagtttt---aacaatgattttttta--tagttttaacaataattatgc-ttacataagatattactaattagaaag--
|| || ||||| ||||| || || |||    || |||| || |||||||||||||| || || ||||| ||| | |||||||| |||||||||||||||||| |||  |  || |     |||  | |||    || |||   | ||  || || ||||  || |   | ||||  || |   | |  |   |||||     | | |     
AACCCTCTTGACTTGCTACCACCAAGCCCTATGGTTCTAGATGATTGGAAGAGGCTTTACTCAAACACCAAATCTAACTTCCGCGAGGTTGCTATTAAAGgtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcag

upper sequence: GRMZM2G029559_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT1G57720.1 (Arabidopsis thaliana), 5'ss of exon 7
AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgtttttaacaatgactatggttacatagttttaacaatgatttttttatagttttaacaataattatgcttacataagatat-tactaattagaaag-
||||| ||||| ||||| || || |||    || |||| || || ||||||||||| || || ||||| ||| |||||||||||||||||||||| ||||||||||| |  |  ||||||   ||||  |  | || | ||  | || ||    ||||    ||| |   || | | |  | |  |  |  |||  || |  
AATCCTCTTGACTTGCTACCACCAAGCCCAATGGTTCTCGATGACTGGAAGAGGCTTTACTCGAACACCAAATCCAACTTCCGTGAGGTTGCTATCAAAGgtatgttat--atgatgacttctgttaattgttctttagaagaaattgttctaggtttatggaatcaacttgttaagaagaaagctacaaaaatccgagaca

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|31406015|gb|CD484747.1|CD484747
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|60341186|gb|DN208159.1|DN208159
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|7304460|gb|AW600399.1|AW600399
EST:     GGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|5108282|gb|AI739995.1|AI739995
EST:     GAGGCTGTATTCTAACNCGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|4885899|gb|AI677019.1|AI677019
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|9732286|gb|BE511038.1|BE511038
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|60400022|gb|DN232829.1|DN232829
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|9461816|gb|BE453919.1|BE453919
EST:     CGTGAGGTTGCTATTAAAG                         GTTTCTGGCACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: CGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|31349931|gb|CD434288.1|CD434288
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|211250756|gb|FL447432.1|FL447432
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|67018044|gb|CO446793.1|CO446793
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|213175370|gb|FM190159.1|FM190159
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTG
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTG
EST: gi|211244390|gb|FL238841.1|FL238841
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|31440873|gb|CD510304.1|CD510304
EST:     GAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|9732285|gb|BE511037.1|BE511037
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|9566225|gb|BE475734.1|BE475734
EST:     ACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: ACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|4753427|gb|AI657337.1|AI657337
EST:     CAACTTCCGTGAGGTTGCTATTAAAG                         GTTTNTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: CAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|60353199|gb|DN220172.1|DN220172
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|88758473|gb|DY542842.1|DY542842
EST:     GAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTTTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|29130485|gb|CB381189.1|CB381189
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
EST: gi|60353205|gb|DN220178.1|DN220178
EST:     GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAG                         GTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT
genomic: GAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 1368

AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 826

AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 515

AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 793

AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgttttt ... gtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCCCCTTGATTTGCTTCCTCCGAGCAAGTTGATTCTTGACGATTGGAAGAGGCTGTATTCTAACACGAAAACCAACTTCCGTGAGGTTGCTATTAAAGgtatgtttttaacaatgactatggttacatagttttaacaatgatttttttatagttttaacaataattatgcttacataagatattactaattagaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaataa