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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctttttcttatcatgtaaatctgtgtattggaggacgtgttgaagtcaaaacaacagtacacaaaaaaatgcgctaatgttttctcatttgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT

Basic information

species Zea mays
transcript GRMZM2G031780_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031780_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g12530.1 (Oryza sativa), 3'ss of exon 9
--cctttttcttatcatgtaaatctgtgtattggaggacgtgttgaagtcaaaacaacagtacacaaaaaaatgcgctaatgttttctcatttgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT
       | ||    |   |||| ||  ||| |        |||   ||   | ||    |         |||   | | ||  |||||||||||   ||||||  ||||||||||| ||||||| ||||||||||| || |||||||||||||||||||| |||||||||||| |||| ||||| |||||||||||  | |
ttgtggctactggctagtcaaatttggatatcgttcttta-gttagtgttttaccacttatctcgtggttaattttcaattgcattctcatttgt-gcgcagGATTTGGATACTGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGT
















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|67025107|gb|CO453856.1|CO453856
EST:     ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAG                         GACCTGGATACTGAAATCATAGTCGCAACAGCAAGGACCCCTGATGCTACA
genomic: ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
EST: gi|211023728|gb|FL449217.1|FL449217
EST:     ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAG                         GACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
genomic: ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
EST: gi|211125159|gb|FL454370.1|FL454370
EST:     TCTCATCGATACAG                         GACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
genomic: TCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
EST: gi|211409698|gb|FL229021.1|FL229021
EST:     ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAG                         GACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
genomic: ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
EST: gi|78089905|gb|DV518279.1|DV518279
EST:     ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAG                         GACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
genomic: ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
EST: gi|94475889|gb|EB704847.1|EB704847
EST:     ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAG                         GACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
genomic: ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
EST: gi|24934308|gb|CA452526.1|CA452526
EST:     ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAG                         GACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA
genomic: ATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACA

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: 49 (upstream exon), 44 (downstream exon)
Score: 164

TGCTATGGCCTCTGCCCTCTCTGAAATGGGTGCTACAGGGAATGATATAAATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

TGCTATGGCCTCTGCCCTCTCTGAAATGGGTGCTACAGGGAATGATATAAATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 93

TGCTATGGCCTCTGCCCTCTCTGAAATGGGTGCTACAGGGAATGATATAAATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 226

TGCTATGGCCTCTGCCCTCTCTGAAATGGGTGCTACAGGGAATGATATAAATACTAATGAATTTGCAAAGGACCTGCGAAAGATATTCTCATCGATACAGgtaatgtttc ... tgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaaaacaacagtacacaaaaaaatgcgctaatgttttctcatttgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT
                           cgctaat  putative branch site (score: 226)
                                   ttttctcatttgtt  CT-rich tract
                acaaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctttttcttatcatgtaaatctgtgtattggaggacgtgttgaagtcaaaacaacagtacacaaaaaaatgcgctaatgttttctcatttgttaagcagGACCTGGATACTGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - catgtaa
- - - - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg