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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccaagtgctcgatcgcgattaatcctcatggcgtctaaagatgaaaaaaaaatctagcgctgttctggtaggagactgacggaattccccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCAAGGTCCCGGCGCTGTCCGAGAACAAGAACGCGGCGTGCCTGGCCGAGCA

Basic information

species Zea mays
transcript GRMZM2G322618_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G322618_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g45060.1 (Oryza sativa), 3'ss of exon 1
-tcccaagtgctcgatcgcgatta-atcctcatggcgtctaaagatgaaaaaaaaatctagcgctgttctggtaggagactgacggaattccccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCAAGGTCCCGGCGCTGTCCGAGAACAAGAACGCGGCGTGCCTGGCCGAGCA
 ||  |  |||  |    | |||  |   | |   |    |||  || | | | |||| |  | | ||    |    |  ||||     | ||| |||||||| | |||  | ||||| |||||||||||||||||||||||  | || ||||| ||||| ||||| |||||||||||||| || || ||| |||| |||||
atctgatatgcatgcaaactattccactgttaaatcaggaaaacttggagatacaatc-attgtt-ttacattgtttgtttgacactgcttcccatttccagGAAGTGATTCACAGCTTCTCAAGGGCATCAACAGCTACAGAGCTTCCCTCAAAGTCCCTGCGCTATCCGAGAACAAGAATGCTGCCTGCTTGGCTGAGCA
















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|211104474|gb|FL141418.1|FL141418
EST:     CTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: CTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|211102006|gb|FL141409.1|FL141409
EST:     CTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: CTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|50334900|gb|CO530026.1|CO530026
EST:     GCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: GCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|71417396|gb|DR804031.1|DR804031
EST:     GCACTGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: GCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|37381470|gb|CF627623.1|CF627623
EST:     TGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: TGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|45567295|gb|CK985501.1|CK985501
EST:     TGCANTGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: TGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|149078591|gb|EE167376.2|EE167376
EST:     GCACTGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: GCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|37374183|gb|CF623433.1|CF623433
EST:     GCCTCTTCCCT-CTGCANNTGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: GCCTCCTCCCTCCTGCA-CTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|211104471|gb|FL141415.1|FL141415
EST:     CTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: CTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
EST: gi|211101999|gb|FL141402.1|FL141402
EST:     CTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACG                         GCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA
genomic: CTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCA

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: 45 (upstream exon), 48 (downstream exon)
Score: 36

GGAGCGCCTTGGTGATCTACGAAGAGGATGAATTCCAGGATCTCCCTCCTCTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCAAGGTCCCGGCGCTGTCCGAGAACAAGAACGCGGCGTGCCTGGCCGAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

GGAGCGCCTTGGTGATCTACGAAGAGGATGAATTCCAGGATCTCCCTCCTCTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCAAGGTCCCGGCGCTGTCCGAGAACAAGAACGCGGCGTGCCTGGCCGAGCA


Block sizes: 33 (upstream exon), 47 (downstream exon)
Score: 7

GGAGCGCCTTGGTGATCTACGAAGAGGATGAATTCCAGGATCTCCCTCCTCTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCAAGGTCCCGGCGCTGTCCGAGAACAAGAACGCGGCGTGCCTGGCCGAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

GGAGCGCCTTGGTGATCTACGAAGAGGATGAATTCCAGGATCTCCCTCCTCTGCGCCCTCGTCCTCGCCTCCTCCCTCCTGCACTGCGCCAGATCCGACGgtaagcttct ... ccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCAAGGTCCCGGCGCTGTCCGAGAACAAGAACGCGGCGTGCCTGGCCGAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaaatctagcgctgttctggtaggagactgacggaattccccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCAAGGTCCCGGCGCTGTCCGAGAACAAGAACGCGGCGTGCCTGGCCGAGCA
                              gactgac  putative branch site (score: 106)
                                         ttccccctttcc  putative PPT
     aaaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccaagtgctcgatcgcgattaatcctcatggcgtctaaagatgaaaaaaaaatctagcgctgttctggtaggagactgacggaattccccctttccagGCAATGACGCGCAGCTCCTCAAGGGCATCAACAGCTACAGGTCCTCGCTCAAGGTCCCGGCGCTGTCCGAGAACAAGAACGCGGCGTGCCTGGCCGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- -caagtgc
- - - - - - - - - - - - - - catggcg
- - - - - - - - - - - - - - - - - - - - - - -aaaaaaa