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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaagggcatttcatacttgtagaatgcctcatgtcacacatctggagcagctttcttacatattatgctataaatccttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG

Basic information

species Zea mays
transcript GRMZM2G135052_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 1
---tttaagggcatttcatacttgtagaatgcctcatgtcacacatctggagca-gctttcttacatattatgctataaatcctt--ctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
   | |   ||||     |||  || |  |    |      |||| ||| |  | | || ||| |   |||| || |  || |||  ||| |||||  | |||||| ||||| ||||| ||||||||||||||||||||||||||||| ||||| |||||||||
ttatcttgtggcaaacattacgagtggggttttac------cacaactgaaaaatggttccttcctacttattctttgcattctttacttgcttttactataacagGTTTGATCGTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG

upper sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G29740.1 (Glycine max), 3'ss of exon 1
-tttaagggcatttcatacttgtagaatgcctcatgtcacacatctggagcagctttcttacatattatgctataaatccttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
 ||| |    |   | || |  | |  |  | | | ||       ||| |  ||  | |  ||   |   |  |   |    | ||| ||||   |  ||| ||||| ||||| ||||||||||||||||||| |||||| || ||||  || ||||||
gtttcaaattaaagc-tagtgtttgtttctcccctttctttatcttggggtcgccatttgccactatcctcactttttttccccttcatttctgttttcagGTTTGATCGTGATTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAG

upper sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
tttaagggcatttca--tacttgtagaatgcctcatgtcacacatctggagcagctttcttacatattatgctataaatccttctttcttttcgt-------gtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
         |||| |  || ||||    |    | | | |      ||| ||     | || |||  | |  |||   |  || ||| | ||| |       ||| ||| ||||||||||||||||||||||||||||||| |||||| || |||||||| || |||
---------atttaagctatttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG

upper sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G24400.1 (Glycine max), 3'ss of exon 1
-tttaagggcatttcatacttgtagaatgcctcatgtcacacatctggagcagctttcttaca-tattatgctataaatcc-ttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
 |  ||    |  |  |  ||||    |  | | | ||       ||| |   || | |  || |||  |   ||   |   ||| ||| |||| | |  ||| ||||||||||||||||||||||||||||||| |||||| || ||||  || ||||||
ttcaaattaaagctagtgtttgtt---tctcccctttcttgaccttggggtctctatttgccactatcctcacattgttttgttccttcatttcttttttcagGTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAG

upper sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
tttaagggcatttcatacttgtagaatgcctcatgtcacacatctggagcagctttcttacatattatgctataaatccttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
|  |  | ||  | |   |  | |  ||  |    |       |   || | | | |||    |||||   ||   |   | |||   ||| |    ||| ||||||||||||||||||||||||||||||| |||||| || |||||||| || |||
tacagtgtcaaattaagataatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG

upper sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
tttaagggcatt-tcatacttgtagaatgcctcatgtcacacatctggagcagctttcttacatatta--tgctataaatccttctttcttttcgtgtaac--agCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
        |||   || | | |  | ||   |   ||    |   |       ||   | |   ||||  | | ||||||   | ||  | ||  |   ||  || ||||||||||| |||||||||||||| |||| |||||| || |||||||| || |||
-----aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttccataaattgattttgttattgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG

upper sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
tttaagggcatttcatacttgtagaatgcctcatgtcaca-catctggagcagctttcttacatattatgctataaatccttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
|  |   | |   |    || |||||||| | | ||  || | | | | | |   ||   |   | | || |  | ||          | |  | |  ||| ||||| || |||||||||||||||||||| |  ||||| || |||||||| ||||||
tggagtaggaaaactggattttagaatgctt-aagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG

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|60358163|gb|DN225136.1|DN225136
EST:     GCACTGCAGCT                         CTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTNTGGCTCCAAGACAG
genomic: GCACTGCAGCTgtgagtcgac ... cgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGT-TGGCTCCAAGACAG
EST: gi|5847380|gb|AW000459.1|AW000459
EST:     GAGAGCTGGACCGACCCCGAGCACGACAAGTTCCTCGAGGCACTGCAGCT                         CTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGT
genomic: GAGAGCTGGACCGACCCCGAGCACGACAAGTTCCTCGAGGCACTGCAGCTgtgagtcgac ... cgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGT

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: 47 (upstream exon), 47 (downstream exon)
Score: 50

AGGAGGGCCCCCGGAGAGTGCGCAAGCCCTACACCATCACCAAGTCGCGCGAGAGCTGGACCGACCCCGAGCACGACAAGTTCCTCGAGGCACTGCAGCTgtgagtcgac ... cgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 121

AGGAGGGCCCCCGGAGAGTGCGCAAGCCCTACACCATCACCAAGTCGCGCGAGAGCTGGACCGACCCCGAGCACGACAAGTTCCTCGAGGCACTGCAGCTgtgagtcgac ... cgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 83

AGGAGGGCCCCCGGAGAGTGCGCAAGCCCTACACCATCACCAAGTCGCGCGAGAGCTGGACCGACCCCGAGCACGACAAGTTCCTCGAGGCACTGCAGCTgtgagtcgac ... cgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 64

AGGAGGGCCCCCGGAGAGTGCGCAAGCCCTACACCATCACCAAGTCGCGCGAGAGCTGGACCGACCCCGAGCACGACAAGTTCCTCGAGGCACTGCAGCTgtgagtcgac ... cgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagcagctttcttacatattatgctataaatccttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
         ttcttac  putative branch site (score: 64)
                               tccttctttcttttcg  putative PPT
                atattatgctataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaagggcatttcatacttgtagaatgcctcatgtcacacatctggagcagctttcttacatattatgctataaatccttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - -gaatgcc
- - - - - - - - - - - - - - - -catgtca
- - - - - - - - - - - - - - - - - - - - - -ctggagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgct