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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacttgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT

Basic information

species Zea mays
transcript GRMZM2G143246_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
gtgagaacttgtttccccaatgcttttcc----ttctcaaccatcttttgggaa-ctccagctaaaaattctgaacacttacaattttgt-tgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT
||| ||| |  |        | |||  ||    ||||     |  || |||    ||   |    ||  |   |||| ||    ||  || |||| || |||| ||||||||||||||||||||  |||||||||| |||||||||||||||||||| |||||||||||||| ||||| ||||||||||| |||||||| ||
gtgcgaaatgttgcttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacattt----ttccgtgtgttattaaagCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT

upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 3
gtgagaacttgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT
                  || | |     ||||  || || ||      ||    |        ||    |  |||| || || |         ||  ||||| ||||| |||||||| || || || ||||| || ||||||||||| || || ||||| ||||| || || || |||||||||||||| | |||
----------------gtaagggtgccttttct-gactatgtt------acctttgtcttgccgtccattcgtttacgatattttc--------agATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCCGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT

upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 3
----------------------gtgagaacttgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT
                      | || || | | || |  | ||  | |     |    | | || ||   |    | ||      |||   |    |    |||    |  ||  ||  ||||| ||||| |||||||| || || || ||||| || |||||||||||||| || ||||| ||||| || || || |||||||||||||| | |||
gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaagggt---gccttttctgactatgttacctttg---tcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT

upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gtgagaact-tgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT
     |   ||  | || | |   | | |||||  || |      |  ||||         |  |||   | | |    ||  |||    ||    |   ||| | ||| || || ||||| ||||||||  | ||||| || |||||||| ||||| |||||||||||||| ||| | || |||||| |||| ||||| ||
gtaatgcttgatttctgctcctggagttctttttttttttcgttcttgtttgatggaagttgtaaaaggctgt-actgattgaaataaaatt----tcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT

upper sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------gtgagaacttgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaac-acttacaa-ttttgtt----------gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT
                              |  |     || || |    |   | ||  ||| | | || | |    |  |      | | ||| |   | | |||||| ||||| |           || |   ||| || || ||||| |||||||| || || |||||||| || ||||||||||||||||||||||| ||||||||| | || |||||||||||||| | |||
gtataagtgtctttctaattcgttgatgtcgctaatttctgatttctatctatctatctatct-atctatatatatatatatatgcacacacatttttttctagttacaagttttggtctttctctgtattttctcagCTCCAGGAGATGGCCCAATTGTATTAGTTTTAGCTCCAACTCGTGAACTTGCTGTTCAGATACAACAAGAAGCAGCTAAATTTGGTGCATCATCGAGGAT

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|71774216|gb|DR972094.1|DR972094
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|78081135|gb|DV509547.1|DV509547
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|149099803|gb|EE185855.2|EE185855
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|76287087|gb|DV026655.1|DV026655
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|94477391|gb|EB706349.1|EB706349
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|93017517|gb|EB643037.1|EB643037
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCATTTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|91053059|gb|EB163477.1|EB163477
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|32840396|gb|CD980077.1|CD980077
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|78074504|gb|DV502938.1|DV502938
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|211108455|gb|FL061195.1|FL061195
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTC-AATTTGTCTTGGTGTTAGCTCCTACACGTGAACTT
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATT-GTCTTGGTGTTAGCTCCTACACGTGAACTT
EST: gi|78077833|gb|DV506262.1|DV506262
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|31359983|gb|CD444340.1|CD444340
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|78120999|gb|DV539383.1|DV539383
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAGTGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|31349821|gb|CD434178.1|CD434178
EST:     GTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCCTTTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: GTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|211108453|gb|FL061193.1|FL061193
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTC-AATTTGTCTTGGTGTTAGCTCCTACACGTGAACTT
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATT-GTCTTGGTGTTAGCTCCTACACGTGAACTT
EST: gi|148938225|gb|EC882515.2|EC882515
EST:     GCTTACCTTTTACCTGCCATTTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: GCTTACCTTTTACCTGCCATT-GTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|149105515|gb|EE291040.2|EE291040
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGGCCCATTTGTCTTGGTGTTAGCTCCTACACG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATT-GTCTTGGTGTTAGCTCCTACACG
EST: gi|148952300|gb|EC898110.2|EC898110
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|149005479|gb|EE040035.2|EE040035
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGGTGT-AGCTCCTACACGTGAACTT
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGG-TGTTAGCTCCTACACGTGAACTT
EST: gi|148931912|gb|EC875118.2|EC875118
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|78083647|gb|DV512040.1|DV512040
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|88751705|gb|DY535846.1|DY535846
EST:     TGCTTACCTTTTACCTGCCATTGTTCGTGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
EST: gi|9732984|gb|BE511736.1|BE511736
EST:     TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTT                         CCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG
genomic: TGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTG

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), 47 (downstream exon)
Score: 121

AGAGGCCGCGACCTTATTGGCATTGCAGAGACAGGATCAGGGAAAACTCTTGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 100

AGAGGCCGCGACCTTATTGGCATTGCAGAGACAGGATCAGGGAAAACTCTTGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 78

AGAGGCCGCGACCTTATTGGCATTGCAGAGACAGGATCAGGGAAAACTCTTGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

AGAGGCCGCGACCTTATTGGCATTGCAGAGACAGGATCAGGGAAAACTCTTGCTTACCTTTTACCTGCCATTGTTCATGTGAATGCGCAGCCTATTCTTTgtgagaactt ... gttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT
                             cacttac  putative branch site (score: 101)
                taaaaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaacttgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA