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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGCGGCGGCGATGGAGCTGCATCATCAGGCGCAGAAGGAGGCTATGGCGCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagatcaaacaaagcgcactccttggctccgcggcggatttcgtcttcttgggcagcagcaccgcacccttctgttccgatttcggatcgtgaaaaggtcgccggggacttaattgtcgggttgctgtgtgcacatag

Basic information

species Zea mays
transcript GRMZM5G887922_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G887922_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g41580.1 (Oryza sativa), 5'ss of exon 2
TTGGCGGCGGCGATGGAGCTGCATCATCAGGCGCAGAAGGAGGCTATGGCGCCGC-AGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagatcaaacaaagcgcactccttggctccgcggcggatttcgtcttcttgggcagcagcaccgcacccttctgttccgatttcggatcgtgaaaaggtcgccggggacttaattgtcgggttgctgtgtgcacatag
   |  |   ||  ||||    | || |||||      | | |   |  | |  | |||||  ||||   || |||||||||||||||||||||||||||| |      | |  |          | ||||  || |||     ||||  |   |   | |  || |  |         ||     || | |                                                    
---GTCGTCTCGCCGGAG----ACCACCAGGCCGGCGGGCATGGAGTATCACTACCAGCAGCATCAGCAGCCTCCCCTCTTCTTGGACTTCTCGCATGGAGATGGAGgtaactgatcgcctttgattcttga-tctgcgtgttttttccccggttcttggattag-attgagatggatggtgttttttgcag----------------------------------------------------
















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|5398727|gb|AI812192.1|AI812192
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGTCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|94472984|gb|EB701942.1|EB701942
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|211011073|gb|FL374942.1|FL374942
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|211434582|gb|FL418946.1|FL418946
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|211334867|gb|FL418387.1|FL418387
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|50328490|gb|CO523616.1|CO523616
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|74240590|gb|DT648504.1|DT648504
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|38688341|gb|CK145372.1|CK145372
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|211533851|gb|FL420810.1|FL420810
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATTGTCGTCG
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCAT-GTCGTCG
EST: gi|211530213|gb|FL396255.1|FL396255
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|148958521|gb|EC904763.2|EC904763
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC
EST: gi|211223962|gb|FL409225.1|FL409225
EST:     GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAG                         ATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCAC
genomic: GCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGC

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: 37 (upstream exon), 46 (downstream exon)
Score: 13

TTGGCGGCGGCGATGGAGCTGCATCATCAGGCGCAGAAGGAGGCTATGGCGCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGCAGTTCTTCTCTCTGCAGCAGCAACCGCAGGCGCAGGGGCCCAAGGTGAT


Block sizes: 39 (upstream exon), 28 (downstream exon)
Score: 2

TTGGCGGCGGCGATGGAGCTGCATCATCAGGCGCAGAAGGAGGCTATGGCGCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGCAGTTCTTCTCTCTGCAGCAGCAACCGCAGGCGCAGGGGCCCAAGGTGAT


Block sizes: 40 (upstream exon), 43 (downstream exon)
Score: 7

TTGGCGGCGGCGATGGAGCTGCATCATCAGGCGCAGAAGGAGGCTATGGCGCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGCAGTTCTTCTCTCTGCAGCAGCAACCGCAGGCGCAGGGGCCCAAGGTGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

TTGGCGGCGGCGATGGAGCTGCATCATCAGGCGCAGAAGGAGGCTATGGCGCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagat ... gtgcacatagATTACGGCGGCGGGAGGAAGCGGCAGCGCGAGGCGGAGCCCATGTCGTCGCAGTTCTTCTCTCTGCAGCAGCAACCGCAGGCGCAGGGGCCCAAGGTGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGCGGCGGCGATGGAGCTGCATCATCAGGCGCAGAAGGAGGCTATGGCGCCGCAGCAGGCTCAGGCTCCGCCCCTCTTCTTGGACTTCTCGCATGGAGgtaagcagatcaaacaaagcgcactccttggctccgcggcggatttcgtcttcttgggcagcagcaccgcacccttctgttccgatttcggatcgtgaaaaggtcgccggggacttaattgtcgggttgctgtgtgcacatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA