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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagataagatccccatctctttgtttcccgtacctcattcttcgccattaaatttatagatttttgtgctgtaaaatcagattgctttatgttgtttgtctgctttgtttgatttctagttgctcgttcaagatcctttacttaatggtgtgcgtgttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGAT

Basic information

species Zea mays
transcript GRMZM2G157068_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 3
gtaag--tagataagatccccatctctttgtttcccgtacctcattcttcgccattaaatttatagatttttgtgctgtaaaatcagattgctttatgttgtttgtctgctttgtttgatttctagttgctcgttcaagatcctttacttaatggtgtgcgt-gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGAT
|||||  ||||||    | |||| ||||    | | |||  | || | |   |       || ||  ||||||||   | |        | |||||    ||||   | |   ||     ||||||  |  | |   |   || ||||||| |||         ||||| ||||||||| ||||| |||||||||||||||||||||||||| || || || ||||||||||| || ||||| |||||||||| |||| ||||||||||||||
gtaagattagatatatcctccatttcttc---ttctgtagttgatacattttc-------ttctatctttttgtgtcatca--------ttcttta----gtttccattccc-gtacagcttctag--ggccat---aaggccattacttactggcaccttccattttgtcagAAAGAACAGCCGTTATAGTGAGAAAGATGCTGCAGTGGTGGTGCGGCAGATGCTCAAAGTGGCAGCTGAGTGCCATCTGCATGGGCTAGTTCACCGAGAT
















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|211195521|gb|FL100645.1|FL100645
EST:     GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA                         AAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
genomic: GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
EST: gi|211195523|gb|FL100647.1|FL100647
EST:     GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCCAA                         AGAAGA-TAGCCGCTATAGTGAGAAAGATGCTGCAATTGGTAGTCCGCCCA
genomic: GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagA-AAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGT-GGTAGTCCGCCAA
EST: gi|149082402|gb|EE171589.2|EE171589
EST:     GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA                         AAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
genomic: GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
EST: gi|211195530|gb|FL100654.1|FL100654
EST:     GCTATGTGAGGGCGGGGAACTATTAGATCGGATTTTGGGCAAA                         AA-GAATACCCGCTATAGTGAGAAAGATGCTGCAGTGGGTAGTCCGCCAA
genomic: GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGG-CAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGG-TAGTCCGCCAA
EST: gi|211195524|gb|FL100648.1|FL100648
EST:     GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA                         AAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
genomic: GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
EST: gi|211195522|gb|FL100646.1|FL100646
EST:     GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA                         AAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
genomic: GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
EST: gi|211195528|gb|FL100652.1|FL100652
EST:     GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA                         AAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT
genomic: GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAAT

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: 42 (upstream exon), 45 (downstream exon)
Score: 47

GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGAT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 102

GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGAT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 122

GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAAgtaagtagat ... gttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttctagttgctcgttcaagatcctttacttaatggtgtgcgtgttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGAT
                             acttaat  putative branch site (score: 122)
                          tttacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagataagatccccatctctttgtttcccgtacctcattcttcgccattaaatttatagatttttgtgctgtaaaatcagattgctttatgttgtttgtctgctttgtttgatttctagttgctcgttcaagatcctttacttaatggtgtgcgtgttttgacagAAAGAATAGCCGCTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT