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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttcctgaatataggaatgtaacatttgtggtatccctgacctgtctgctgcttaacactgcaattaaaaagtatatgtgaaccttgacttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 11
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 3'ss of exon 10
-aggttcctgaatataggaatgtaacatttgtggtatccctgacctgtc-tgctgcttaacactgcaattaaaaagtatatgtgaaccttgacttttg-ctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG
 | |||  ||| |  |    || | | |          |  |   | |  | ||||| |  | |   |||    ||| | ||    | ||||| ||||  |||||||||||||||| || ||||| |||||||||||||||||||| |||||||| || |||||||| ||||||
catgttt-tgattggatccttgaatcgtacagaactctctagtgatattgtactgctaattattaatatttgctagtgtctg--gtctttgacctttggttagAAATCCCATATTTTCGTGAGGTTATTGTTATGGCAACAACATGCGACATGTGCGGCTATCGCAACTCAGAG
















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|211367141|gb|FL432366.1|FL432366
EST:     AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCGACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|211282780|gb|FL192971.1|FL192971
EST:     AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|30306974|gb|CD001647.1|CD001647
EST:     AACATGTGGAGCCTG-GG-ACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|78085694|gb|DV514087.1|DV514087
EST:     AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|31611962|gb|CD568584.1|CD568584
EST:     AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|37401209|gb|CF637968.1|CF637968
EST:     GAGCCTGTGGAACAGAATGTGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: GAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|67020485|gb|CO449234.1|CO449234
EST:     AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|60395671|gb|DN228541.1|DN228541
EST:     TGGAACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: TGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|29946582|gb|CB816222.1|CB816222
EST:     AACATG-GGAGCCTG-GGAACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|211282782|gb|FL192973.1|FL192973
EST:     AACATGTGGAGCCTGTGGAACARAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|28568977|gb|CB280852.1|CB280852
EST:     AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|211367140|gb|FL432365.1|FL432365
EST:     AACATGTGGAGCCTGTGGAACAGAATGCGTCMCACGTTTCTTTGCGACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
EST: gi|60357973|gb|DN224946.1|DN224946
EST:     AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAA                         AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT
genomic: AACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGT

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), 45 (downstream exon)
Score: 374

GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 191

GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 110

GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 185

GTTGATACTTTACCATCAACATGTGGAGCCTGTGGAACAGAATGCGTCACACGTTTCTTTGCTACAAgtatcctttc ... cttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgctgcttaacactgcaattaaaaagtatatgtgaaccttgacttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG
                                     aaccttgac  putative branch site 
                                             cttttgct  CT-rich tract
                   aattaaaaagtatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttcctgaatataggaatgtaacatttgtggtatccctgacctgtctgctgcttaacactgcaattaaaaagtatatgtgaaccttgacttttgctagAAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG

- gttcctg
- - - - - - - - - - - -acatttg
- - - - - - - - - - - - - - - - - atccctg
- - - - - - - - - - - - - - - - - - - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgca