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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgcccttgacgaagttttctaagatgctattagtacctttggttattgtgatgttacattcccaactttacattttctatcaagatgttgtaatct...

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g30460.3 (Oryza sativa), 5'ss of exon 6
ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattg-cccttgacgaagttttctaagatgctattagtacctttggttattgtgatgttacattcccaactttacattttctatca--agatgttgtaatct-
||||| |||||||||||||| ||||||||||||||||| ||||| || ||||||||||| ||||||||||||||||| || || ||| || ||| | ||| || | | || || | || | || | | | | || ||| | || | | || |
ATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGGgtaatgtcctttgtttgagctttgtctttggcttgaagcaa----gatttccatgttatttccttaaaatcagtgctccctccgtcataaaatatagcaactta

upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G34480.1 (Glycine max), 5'ss of exon 3
ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgcccttgacgaagttttctaagatgctattagtac-ctttggtta--ttgtgatgttacattcccaactttacattttctatcaagatgttgtaatct-
||||| || || ||||| ||||||| || |||||||| ||||| || || || |||||||| |||||||||||||| | ||| |||| || | | || | ||||| | ||| || | | || || ||| || || | | | || |
ATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGGgtaattttctttttcttcctttc-aattttttcttcccatgttttggatggcctgtaatttaagctttatgcacttcagtttcttacca---tctagaaaatta

upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G33080.1 (Glycine max), 5'ss of exon 7
ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgcccttgacgaagttttctaagatg-ctattagtacctttggttat-tgtgatgttacattcccaactttacattttctatcaagatgttgtaatct-
||||| || || ||||| ||||||| || |||||||| ||||| || || || |||||||| |||||||||||||| | ||| | |||| | | || | || | | | ||| || | | || | || ||| || || | | | || |
ATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGGgtaattttctttttcatcctttcaattttttcttcccatgttttggatgacctgtaatttaagctttatatacttcagtttcttacca---tctagaaaatta

upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G34480.1 (Glycine max), 5'ss of exon 7
ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgcccttgacgaagttttctaagatgctattagtacctttggttattgtgat---gttacattcccaac--tttacattttctatcaagatgttgtaatct
|| || || |||||| | ||||||||||||| || || ||||| || ||||| ||||| || |||||||||||||| | || | | | | ||| | | ||| | | ||| | || | ||| || | || | |||| | | | | |
ATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGGgtaatagtttttcccta-tactgaaagccattcattgtaaatgttgtttgtttggtatggttgagttgtctacaatctacactgtttgtttgaccaagatg----

upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT3G52200.1 (Arabidopsis thaliana), 5'ss of exon 11
ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgcccttgacgaagttttctaagatgctattagtacctttggttattgtgatgttacattcccaactttacattttctatcaa--gatgttgtaatct------
|| || || |||||||| ||| ||||||| || ||||| ||||||||||| || |||||||||||||||||||||||| | | | | | |||| | | | | | | || || | | | | |||| ||||| ||| ||| |
ATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGGgtataact--------aacatcttgtcgtcttatttctttttctaggcagtatgttgatgttcattctatatagcattcactatctgtggatattgcttcttttcttg

upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 5'ss of exon 7
ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgcccttgacgaagttttctaagatgctattagtacctttggttat-tgtgatgttacattcccaactttacattttctatcaagatgttgtaatct--
|| ||| ||||| || |||| || ||||| || || ||||| || |||||||||||||| |||||||||||||| | | || | ||| |||| | | | | || | ||| | || | | | || | ||| |||| | || | || | |
ATTGAGCCAGGTGACGTTCTATGCGAAATAGAGACAGACAAAGCTACCCTTGAGTTTGAAAGTCTTGAAGAGGGgtaattctgttttct---tttcctaaaaacaagctgattttatatattttgtgtagtaatagaatgtaatattgagattagctattatagtgatatattgtct

upper sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 5'ss of exon 11
ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct-tgacgaagttttctaagatgctattagtacctttggttattgtgatgttacattcccaactttacattttctatcaagatgttgta-atct
||||| || ||||||||||||||||||||||| || || |||||||| ||||| |||||||| |||||||||||||| || || |||| | | || ||| | ||||| | | | | || || || | | | || || | || ||| || | ||
ATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGGgtaatgttctatgacaatgccttataatactctattgctttacaca-taaataaataaataaataaataaataaataatt-ctttgaaaatgccatagaact

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|71433814|gb|DR814864.1|DR814864
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
EST: gi|76924992|gb|DV170232.1|DV170232
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
EST: gi|148945041|gb|EC890225.2|EC890225
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
EST: gi|149003162|gb|EE038900.2|EE038900
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
EST: gi|211038407|gb|FL104474.1|FL104474
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGGAAGGTTCTAAAGATGTTCAANGTT
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTG-AAGGTTCTAAAGATGTTCAA-GTT
EST: gi|149028361|gb|EE286119.2|EE286119
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
EST: gi|88758154|gb|DY542295.1|DY542295
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
EST: gi|211038406|gb|FL104473.1|FL104473
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
EST: gi|211431303|gb|FL159147.1|FL159147
EST:     CTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: CTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
EST: gi|211038408|gb|FL104475.1|FL104475
EST:     GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAAGG                         GTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG
genomic: GAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGG

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), 49 (downstream exon)
Score: 157

ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGGACAACCCATTGCTGTTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGGACAACCCATTGCTGTTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGGACAACCCATTGCTGTTACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 204

ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgccct ... aatgcttcagGTATTTGGCCAAGATTTTAGCACCTGAAGGTTCTAAAGATGTTCAAGTTGGACAACCCATTGCTGTTACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGGgtattgcccttgacgaagttttctaagatgctattagtacctttggttattgtgatgttacattcccaactttacattttctatcaagatgttgtaatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG