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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggttcgtaggtttcggttggtatcttaactcgatttgggatcctttttcttttgggtttcgatttcatccattttgcagcccagccggctgtgc...

Basic information

species Zea mays
transcript GRMZM2G101480_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101480_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggttcgtaggtttcggttggtatcttaactcgatttgggatcctttttcttttgggtttcgatttcatccattttgcagcccagccggctgtgc-
|| |||||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||  ||  | |        |         ||   ||    ||  |||    ||   || |  ||||  | || |    |||| |  | |   || | |   
GTGGTGCGGAAGAAGGCGCCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCCCGCCGCTCCGGCGCCGAGATCGAGACCATGAAGAAGTgtgcgtactactgcctcccccaccccctcctacccttttcttttgatttgattcgattcgcttttccctctccttttctttg-aatcgaaggggttctttt

upper sequence: GRMZM2G101480_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G42900.1 (Glycine max), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggttcgtaggtttcggttggtatcttaactcg--atttgggatcctttttcttttgggtttcgatttcatccattttgcagcccagc-cggctgtgc
||  | || |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||| |||||||||||||| || ||||| ||| | || || |||   |  | |  |          | |   | || |     | |    | |||||  ||||   | | |  |     | | |||   |   |      ||   
GTCCTCCGCAAGAAGGCTCCCACTGCCGCCGCCAAGAAGGATGAGAAAGCCGTCAACGCCGCCCGCCGCTCCGGCGCCGAAATCGAAACCCTAAAAAAATgttcct--tcccaaaaccctcaccgattgatcaatttattgtcttttcttcttttgtttttaaatataggatctgaacttcttgtttcttgggattattgca-

upper sequence: GRMZM2G101480_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G42890.1 (Glycine max), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggttcgtaggtttcggtt----ggtatcttaac--tcgatttgggatcctttttcttttgggtttcgatt-tcatccattttgcagcccagccggctgtgc
||  | || |||||||| ||||||||||| ||||||||||| ||||| |||||||||||||| |||||||| ||||| || ||||| ||| | || ||||||  ||  | | ||        ||       ||  |||   |  || |  ||    || |   | | || | |||| || | || ||   ||      |        
GTCCTCCGCAAGAAGGCTCCCACCGCCGCCGCCAAGAAGGACGAGAAAGCCGTCAACGCCGCCCGCCGCTCTGGCGCCGAAATCGAAACCCTAAAAAAGTgttcgt--tccctaaaccctcattcaaaaaaatagtaatagtaaatcttcgaatagttgttcgtcgcgtgttgattgtcttacaattataagtttcttctaa-----

upper sequence: GRMZM2G101480_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G15420.1 (Glycine max), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggttcgtaggtt--tcggttggtatctta-actcgatttgggatcctttttcttttgggtttcgatttcat--ccattttgcagcccagccggctgtgc
||  | || |||||||| ||||||||||| ||||||||||| ||||| |||||||||||||| || |||||||||||||| || || ||| | || ||||||  ||       |   |  |||      | | || | |  || |  ||    || |   | | || | ||||   |  | | | |  |   |  |   |     
GTCCTCCGCAAGAAGGCTCCCACCGCCGCCGCCAAGAAGGACGAGAAAGCCGTCAACGCCGCCCGGCGCTCCGGCGCGGAAATTGAAACCCTAAAAAAGTgttcgttcccaaaaccctcatcgaaaaaaaacatataataaatattcgaatagttgttcgtcgcgtgttgattatctgacaaatataaatttcttctcac-----

upper sequence: GRMZM2G101480_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G15410.1 (Glycine max), 5'ss of exon 1
------------------------------GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggttcgtaggtttcggttggtatcttaactcgatttgggatcctttttcttttgggtttcgatttcatccattttgcagcccagccggctgtgc
                              ||  | || |||||||| |||||||| || || |||||||| ||||| |||||||||||||| |   |||| |||  | | ||| | ||| | || |||| |  ||  | |  |        | |        | | |||  |  |    || ||||   |                                       
GGCCCTCTTTCTCTGGATTGGGAACCCGTCGTCCTCCGCAAGAAGGCTCCCACCGCTGCCGCTAAGAAGGACGAGAAAGCCgtcaacgccgcccaatgctctggcttg-aaatcaaaaccctaaaaaagtatttgt--tgccaaaaccctaatcg--------aattgatcagttaattgttgtcttcacga--------------------------------------

upper sequence: GRMZM2G101480_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv19s0014g01260.t01 (Vitis vinifera), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggttcgtaggtttcggttggtatcttaactcgatttgggatcctttttcttttgggtttcgatttcatccattttgcagcccagccggctgtgc-------
||  | ||||||||| | | || |||||| ||||||||||| ||||| |||||||||||||| || |||   ||||| |||||||||||  | ||||||||||     |||     ||||  ||  | ||   | |   ||| |     ||||||       | |        |  | |  | | |  |      | |         
GTGATCCGGAAGAAGCCTCTCAACGCCGCCGCCAAGAAGGACGAGAAAGCCGTCAACGCCGCCCGTCGCATGGGCGCCGAGATCGAGACTGTCAAGAAGTgta-----ttccc--ctttctctttctttccccattttttttcgttgtttttttcgaagaaatctttggagggtagaatgagaatcgaaaaatattttttattttcc

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|211150712|gb|FL424943.1|FL424943
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211199840|gb|FL414699.1|FL414699
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211134616|gb|FL369498.1|FL369498
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|74237600|gb|DT645514.1|DT645514
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGA
EST: gi|87154044|gb|DY398833.1|DY398833
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|14701255|gb|BI233673.1|BI233673
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211297066|gb|FL414882.1|FL414882
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|76909113|gb|DV163229.1|DV163229
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         TCAACGCTGGTATGAAACA-GGCGGCGTCCAG
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAA-CAAGGCGGCGTCCAG
EST: gi|211171174|gb|FL157590.1|FL157590
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211426583|gb|FL408876.1|FL408876
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211221428|gb|FL386095.1|FL386095
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|51592547|gb|CV071693.1|CV071693
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCCCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
EST: gi|211508672|gb|FL378338.1|FL378338
EST:     CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGT                         ACAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCA

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 3 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 6

GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC


Block sizes: 48 (upstream exon), 31 (downstream exon)
Score: 3

GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 9

GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggtt ... ttatctgcagTCAACGCTGGTATGAACAAGGCGGCGTCCAGCGGCACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTGCGGAAGAAGGCACCCACCGCCGCTGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCTCCGGCGCGGAGATCGAGACCATGAAGAAGTgtaagtggttcgtaggtttcggttggtatcttaactcgatttgggatcctttttcttttgggtttcgatttcatccattttgcagcccagccggctgtgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT