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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA

Basic information

species Zea mays
transcript GRMZM2G033208_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggtt--gctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
||||||  |||   ||   |  |   | |           |  ||||    |  ||| |     ||| |||| |||||| | | |||||  | | || ||| ||||||||||||||||| || ||||| |||||| |||| ||||||||||||||||||||||| || ||||||||||| ||||| ||||| || || ||
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
    |||   |  |  |||||  | ||   |  | ||    | || || ||  | |    ||| |     |||  | ||||  | | ||  |||  ||| |||||||||||||| || |||||||| ||||| || ||||| |||||||||||| ||||||| || || ||||||||||||| |||||| || |||||
----gttagatgtttcattggtttatg---ttactgt-tatcatggtgagcctttttg--ctgtgttctgttgcttatcct-cacgttt--tgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 2
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgt-gcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
|| || | |    |  | |  | | | |   |   ||    |||  | |  | |||     |  |    |||   | |||  ||| | |  | | | ||| |||||||||||||| || |||||||| ||||| ||||| ||||| ||||||||| |||||||  | | |||||||||||||| |||||| || |||||
gtttgatatgagttagagtttg-tataatagaatagtaattctttttattttttatttttatt-gtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
    |||   |  |  ||| |  | ||   | |   |    | |  || ||  | |    ||| |     |||  | ||||   || ||  |||  ||| |||||||||||||| || |||||||| |||||||| ||||| |||||||| ||| ||||||| || || ||||||||||||| |||||| || |||||
----gttagatatttcattagtttatgttattgttat----catagtgagcctttttg--ctgtgtcctgttgcttatcct-cgtgttt--tgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 2
gtctgt--tttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgag---aaagtttgggtttcctatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
|| ||   |||    ||| ||||  | ||  | |   |              || | || |||||     | | ||  | | ||   | ||| |||| |||||| |||||||| || || ||||| ||||| ||||| || || ||||||||||||||  |||||||  | |||||||| |||||   |||  | ||||||||
gtttgagattttgcttcttttggcttatggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGAGAAGCATTTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCA

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 2
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgt-gcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
          ||  ||  ||  |  ||||  |       |  |  ||||    || ||  || | ||     ||   |  | | |  ||||| |   ||| ||||||||||||||||| |||||||| ||||| |||||   ||  ||||||||  |||||||  | |||||||| ||||||| |||||| ||||||||
---------gttggctgctgttccttgaa--acttaattcaatgtctgtatgttagaatgctaataa---ccggtccttatgtgttattgcttttatagGCCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGTTTGGCCGCTGTGGAGAAGCATTTGGCTGCAAGATTCAACAAACCTGACAATGAGATTGTCGACCA

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtt--tgggtttcctatatggttgc---tgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
    |||   ||||    | |  ||| || |  | ||     ||||||  |  || || |  |     |||  |    |    | ||  || |   |||| ||| ||||||||||||||||| |||||||| ||||| ||||| ||||| |||| |||| ||||||| || |||||||| || |||| |||||| || || ||
----gttagattctagtcttgaatgttaaat--ctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA

upper sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP06856 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcc-----tatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
| | |  |      ||  | |  || |    |||  || | |  ||    ||||  ||| ||||      |      |||     | ||    ||||  | ||| || || || |||||||||  ||| ||||| ||  ||||  | ||||||   |||||||||||||||||||||||||| |||    ||  | |||   |
ggccggatgtgcggcttgtagagtgcgcggaagcactgtcgcccgcc---ctgtgaaaacctgatcgtcctgacccgtcccctcgtttactcctgctccgtagGTCCCCTGGGCCAGGGTATCTGCAACGCCGTCGGCCTGGCCGTGGCTGAGGCCCACCTGGCTGCCCGCTTCAACAAGCCGGACGTCAAGCCCATCGTGGA

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|211471115|gb|FL255208.1|FL255208
EST:     TTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: TTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|149086592|gb|EE176136.2|EE176136
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|71311290|gb|DR791959.1|DR791959
EST:     ACCGGGCCACCNTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|148999663|gb|EE036652.2|EE036652
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|148938610|gb|EC882938.2|EC882938
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|149074164|gb|EE162522.2|EE162522
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|148950704|gb|EC896296.2|EC896296
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|8383193|gb|BE056136.1|BE056136
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|149004965|gb|EE039481.2|EE039481
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCGAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGCCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|76281986|gb|DV021554.1|DV021554
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|76285424|gb|DV024992.1|DV024992
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|8318856|gb|BE025496.1|BE025496
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|32921472|gb|CF026284.1|CF026284
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|78079231|gb|DV507643.1|DV507643
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|71311289|gb|DR791958.1|DR791958
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
EST: gi|8318855|gb|BE025495.1|BE025495
EST:     ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG                         GGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA
genomic: ACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGA

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: 49 (upstream exon), 48 (downstream exon)
Score: 354

GAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1437

GAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 664

GAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1221

GAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCGgtctgttttc ... tgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA
        tgtataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtttgggtttcctatatggttgctgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC