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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaggcttcaattttattaacaaggattttgttcaccttgtatgagtgcattaacattttgctcaagcctttatgtaaatactttgttgtatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG

Basic information

species Zea mays
transcript GRMZM2G087212_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 8
-tagaggcttcaatttt--attaacaaggattttgttcaccttgtatgagtgcattaacattttgctcaagcctttatgtaaatactttgttg--tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG
| | |||| || | ||| |||| || | | || | || || |||| | | ||| ||||| || | | |||||| ||| ||||||||||||||||| |||||||| ||||||||||| |||||||||||||| |||||||||||||||||||| ||||| ||||||||||| |
ttttatctttcatttctggattgacaataatc--agtaatgtttgttcagctagctagtatttctttgcaccctac---taaatgctgtacttcttatttgtcagACGAGGAGCTATCATCACGACCTTCATCGTGTGCTACGCCCTTACATCTTTCATTTCTGGATATGTTAGTGGTGGCCTCTACTCAAGGAATGGCG

upper sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 8
-----tagaggcttcaattttattaacaaggattttgttcaccttgtatgagtgcattaacattttgctcaagcctttatgtaaatactttgttgtatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG
|| ||| ||| || | ||| | || | | || | | || | | |||||||| | || || || ||| || |||||||| || |||||||||||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||| || | || ||| | ||||| |
tatcactgaatgttccattcctctagttttcctattgactatattttttttgtcgact--tcttctcccttcattattatgtaagt--ttccttcaatgtgc-agACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGTAATGGGG

upper sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 8
--tagaggcttcaattttattaacaaggattttgttcaccttgtat-gagtgcattaacattttgctcaagcctttatgtaaata--ctttgttgtatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG
| | ||| | || || || || || | ||| |||| | | || | || | | |||||| | ||| ||| | | |||||||||||| || |||| || ||||||||||| || ||||| ||||||||||| ||||| ||||| ||||| || | || ||| | ||||| |
gttggctatttctacttcat--actag---ttggaacactttgtgttgtttgttcctttctctttcgttgattatcatgtaagtttccttaattgcttgtctcagGCGAGGAGCCATTGTCACTACTTTCATTGTGTGTTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGAAATGGGG

upper sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 8
---tagaggcttcaattttattaacaaggattttgttcaccttgtatgagtgcattaacattttgctca--agcctttatgtaaatacttt-gttgtatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG
| | ||| | || || || || || | ||| |||| | || || | | || | |||||| | | || ||| | | |||||||||||| |||||||| || ||||||||||| || ||||| |||||||| || ||||| ||||| ||||| || | || ||| | ||||| |
agttggctatttctacttcat--actag---ttggaacactttgtgtt-gtttgttcctttctctcttgttgattgtcatgtaagttccttcattgcttgtctcagGCGAGGAGCCATCATCACTACTTTCATTGTGTGTTATGCTCTCACATCTTTTATTTCTGGTTATGTGAGTGGGGGGATGTACTCACGAAATGGGG

upper sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 8
------tagaggcttcaattttattaacaaggattttgttcaccttgtatgagtgcattaacattttgctcaagcctttatgtaaatactttgttgtatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG
| | ||| | | | | | | | || || | | | | | ||| | || | | | || | | | || || || ||| || |||||||| || |||||||||||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||| || | || ||| | ||||| |
tatcactgaatgctcccttcctct----agttttcctattgactatatcttt-tatgtcaacttcttctcccatcattattatgtaactttccttcaatgtgc-agACGAGGAGCCATAGTCACAACCTTCATTGTTTGCTATGCTCTCACATCTTTCATTTCTGGTTATGTGAGTGGGGGAATGTACTCACGTAATGGGG

upper sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 8
tagaggcttcaattttattaacaaggattttgttcaccttgtatgagtgcattaacattttgctcaagcctttat-gtaaatactttgttgtatttgc-cagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG
||| | | | | | | || | | | || | ||| || |||||| ||||| || | |||||||||||||| |||||||||||||| || |||||||| || ||||| ||||| || | || || | || | ||
----------------------------------------gtaagtatctgtcaccctgcggccgaggtgctcatcgctcgcctcgccctgtgttgatgcagGCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTCAGTGGCGGGTTTTACTCGCGAAACGATG

upper sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ37593 (Selaginella moellendorffii), 3'ss of exon 8
tagaggcttcaattttattaacaaggattttgttcaccttgtatgagtgcattaacattttgctcaagcctttat-gtaaatactttgttgtatttgc-cagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG
||| | | | | | || | | | || | | | || |||||| ||||| || | |||||||||||||| |||||||||||||| || |||||||| || ||||||||||| || | || || | || | ||
----------------------------------------gtaagtatctgtcacgctgcggccgaggtgctcatcgctcgcctcgccctttgttgatgcagGCGGGGAGCAATAGTGACAACCTTCATTGTATGCTACGCTCTTACGTCATTCATCTCCGGTTATGTTAGTGGCGGGTTTTACTCGCGAAACGATG

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|32930509|gb|CF035321.1|CF035321
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCGACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|32933279|gb|CF038091.1|CF038091
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|33094118|gb|CF054112.1|CF054112
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGCTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|71428339|gb|DR809389.1|DR809389
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|32932276|gb|CF037088.1|CF037088
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|211036620|gb|FL478462.1|FL478462
EST:     YTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTYATATGTTGG                         GCGAGGAGCTATCATCWCAACCTTCATTGTGTGGTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|71764885|gb|DR962822.1|DR962822
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTACTACGCTCT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCT
EST: gi|15199064|gb|BI423636.1|BI423636
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|32930445|gb|CF035257.1|CF035257
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTATCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|32932743|gb|CF037555.1|CF037555
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
EST: gi|32930966|gb|CF035778.1|CF035778
EST:     CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGG                         GCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT
genomic: CTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTT

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), 36 (downstream exon)
Score: 261

GCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTGGCACTCAGCTGGCGGCTCTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG


Block sizes: 49 (upstream exon), 28 (downstream exon)
Score: 149

GCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTGGCACTCAGCTGGCGGCTCTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

GCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTGGCACTCAGCTGGCGGCTCTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 389

GCCAGGTGTTTCTTTCTGCCCTAGTTGGTATTGGCACTCAGCTGGCGGCTCTTATCCTGCTTGTGATTGTGTTGGCCATTGTTGTCATGTTATATGTTGGgtaagctcat ... tatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgcattaacattttgctcaagcctttatgtaaatactttgttgtatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG
    cattaac  putative branch site (score: 389)
 tttatgtaaatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaggcttcaattttattaacaaggattttgttcaccttgtatgagtgcattaacattttgctcaagcctttatgtaaatactttgttgtatttgccagGCGAGGAGCTATCATCACAACCTTCATTGTGTGCTACGCTCTTACATCTTTCATCTCTGGATATGTTAGTGGTGGTCTCTATTCAAGGAATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -gcttcaa
- - - - - - - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - ttgtatg
- - - - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgttg