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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC

Basic information

species Zea mays
transcript GRMZM2G038126_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 5
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcct----caccctgaa--tgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
| ||| ||| | || | ||| | | | | | | ||||| | || | ||| | | ||||| | | | || ||||||| ||||||||||||||||||||||||||||| ||||||||||| |||||||| || ||||| ||||||||||||||||| |||||||| |||||||||||
tttactctctgc-tcagcttttgctcaataa----atactgtaagcatttatattcgctttcccttgtgctgttctgaaattcattgtgatgttctgttttt-cagATTGCTGCTATCTGTCAAGAAGCTGGTATGCATGCTGTGCGCAAAAATCGGTATGTTATCCTCCCCAAGGACTTCGAGAAGGGTTACCGAACCAATGTCA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 5
aatgctccttgcattagttattggttattgacctgac-aatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtt-tttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
| | | || || || | | | ||||| || || | | | | | || | | | | | || || | | ||||| | ||||| |||||||||||||| ||||||||||| ||||| || |||||||||| || ||||||||||| |||||||| ||| | || |||
agaggtagctgtgataaataagaaagacgattaagtctaatgtcaa--taaatgtgatatatataaacagttttattatttgatgaatgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCCAAGGACTTCGAGAAGGGTTACAGGACAAACGTGA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 5
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattat-----gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
|| | | || | || | |||| | | | | | |||| | | | | | | | | || | || || || | ||||| | ||||| |||||||||||||| ||||||||||| ||||| || |||||||||| || || |||||||| |||||||| || | || |||
--tg-tgaatatatgcctgatagaagattg--ccatctctacaggtctttgtaatatatatatatataaacagttttatcatttgatgattgttggtgcctgcagATATCAGCTATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCAAAGGACTTCGAGAAGGGTTATAGGACAAACGTGA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 5
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctt--tttttcctcaccctgaatgctcctcgcattat--gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
||| | | | | || | || | | || ||||| |||| | | | | || | | | | | ||| | || | ||||| || || || |||||||||||||| ||||||||||| ||||| || |||||||||| || || |||||||| |||||||| ||| | || |||
aataagttaaatgtcaataaatg-tgatatatatat--atataaaaacaggtctttgtaatatataaacagttttattatttggtg-attgttggtgcctgcagATAGCAGCCATTTGTCAAGAAGCTGGAATGCATGCTGTTCGCAAGAATAGATATGTCATACTGCCGAAGGACTTCGAGAAGGGTTACAGGACAAACGTGA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 5
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcat----tatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
|| | | | | || |||| | | | | | | ||| | ||| | ||| || | | || | | | | |||||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||| || ||||||||||||||||||||||| || ||||||||
aaccagcggagaaactctgataggttcccaaggtt-tttcattatttcaaataaacgaatttctcatg---tgagtgtttttaacacaatctgtacgtatgcagATTGCTGCTATTTGTCAAGAAGCTGGGATGCATGCTGTTCGCAAGAACCGATATGTAATTCTCCCCAAGGACTTTGAGAAGGGTTATCGAACCAATGTGA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 5
aatgctccttgcattagttattggt--tattgacctgacaatgtaa-aattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
||| | | || || | | | |||| |||| | | | | | | | | | | ||| | | ||| |||||| |||| |||||||| || ||||| |||||||| ||| | || || || ||||| || | |||||||| ||||||||||||||| || |||||
tatgttgagttcagctgtaaattatagtattaggtcaggtctgtattagctggatttgtatgtgctgcatatctgatatgattgatttgtcatg---acgcagATTTCTGCCATCTGTCAGGAGGCTGGTATGCATGCAGTCAGAAAGAATCGTTATGTGATTTTGCCCAAGGATTTTGAGAAGGGCTACAGATCCAACGTCA

upper sequence: GRMZM2G038126_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 5
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC----
||| | || ||| | | | |||||| ||| | ||||||||||| || |||||||| || ||||||||||| || | || || || || || || || |||||||||||||||||||||||| | ||||||
----------------------------------------------gtagagagccgtttgtcttgggcttta---ctctgacgcatttcctttatccagATTGCTGCGATATGTCAAGAGGCAGGCATGCATGCGGTGAGGAAGAATCGCTACGTTATTCTTCCCAAGGACTTTGAGAAGGGCTACAGGACCAACGTGA

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|67017682|gb|CO446431.1|CO446431
EST:     TTGATTTGGAAGACTATGTTTNCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAAACTGGCATGCATGCTGTNNCGCAAAA
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTC-CGCAAAA
EST: gi|32835304|gb|CD974982.1|CD974982
EST:     TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA
EST: gi|6194636|gb|AW146740.1|AW146740
EST:     TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAANCTGGCATGCATGCTGGCCGCAAAAACCGA
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA
EST: gi|32846623|gb|CD986304.1|CD986304
EST:     TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGA
EST: gi|18964972|gb|BM661316.1|BM661316
EST:     TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGAT                         ATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCT
genomic: TTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCT

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: 48 (upstream exon), 48 (downstream exon)
Score: 130

GTCTGCACTGCCAAAATGAACCTGAGTGACGAGGTTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 165

GTCTGCACTGCCAAAATGAACCTGAGTGACGAGGTTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 167

GTCTGCACTGCCAAAATGAACCTGAGTGACGAGGTTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 217

GTCTGCACTGCCAAAATGAACCTGAGTGACGAGGTTGATTTGGAAGACTATGTTTCCAGACCGGATAAGATCAGTGCTGCTGATgtgagtctcg ... gtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC
                 tcctcac  putative branch site (score: 217)
 tgttttt  putative PPT
 attatgtttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgctccttgcattagttattggttattgacctgacaatgtaaaattaggtaacctttttttcctcaccctgaatgctcctcgcattatgtttttacagATTGCTGCTATCTGTCAAGAAGCTGGCATGCATGCTGTCCGCAAAAACCGATATGTCATCCTCCCCAAGGACTTTGAGAAGGGCTACCGAACCAAC

- tgctcct
- - -tccttgc
- - - - - - - - - - - - - - tgacctg