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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctccctcttgtttctctgtctgctgtcattaagtttacctttgaatggatgaatgctaacttagcatataatctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTTTACCACG

Basic information

species Zea mays
transcript GRMZM2G053019_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053019_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 2
gtgagttctccctcttgtttctctgtctgctgtcattaagtttacctttgaatggatgaatgctaacttagcatataatctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTTTACCACG
  | |  |    |    ||  | ||||||    || |    | | |||  | || ||||    | || | | | ||  | | ||||| ||||||||||||||||||||||||||||||||||||||||| |  || ||| | | |
--gtgcgccagtttcccttcttttgtctggctacaattttctcaacttacactgcatga----tgacat-gtaaatcctttgtgcagCGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCCGCAGCATTTTCTATG
















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|71775343|gb|DR973221.1|DR973221
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|148962609|gb|EE013495.2|EE013495
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|148967401|gb|EE018626.2|EE018626
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|148986910|gb|EE030719.2|EE030719
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|71440817|gb|DR821867.1|DR821867
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|211172020|gb|FK988437.1|FK988437
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCACCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|32799699|gb|CD951935.1|CD951935
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCACCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|78108045|gb|DV526463.1|DV526463
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|148941186|gb|EC886070.2|EC886070
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|71440311|gb|DR821361.1|DR821361
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|148972016|gb|EE022842.2|EE022842
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|211172010|gb|FK988427.1|FK988427
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCACCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|76019253|gb|DT946423.1|DT946423
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|76292083|gb|DV031651.1|DV031651
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|74235753|gb|DT643667.1|DT643667
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|78085071|gb|DV513464.1|DV513464
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|148940610|gb|EC885417.2|EC885417
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|211173687|gb|FK988440.1|FK988440
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCACCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|211173691|gb|FK988444.1|FK988444
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCACCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|211172016|gb|FK988433.1|FK988433
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCACCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|211173695|gb|FK988448.1|FK988448
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCACCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCG
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCG
EST: gi|148932254|gb|EC875785.2|EC875785
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|149080112|gb|EE169131.2|EE169131
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|76020426|gb|DT947596.1|DT947596
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
EST: gi|148932491|gb|EC876253.2|EC876253
EST:     TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACAT                         TGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT
genomic: TCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTT

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), 47 (downstream exon)
Score: 122

GAGCAAAAGGCTTTGCAAGCATGTCATCTTCGACTGCCAATGAGAATATGTCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTTTACCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

GAGCAAAAGGCTTTGCAAGCATGTCATCTTCGACTGCCAATGAGAATATGTCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTTTACCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

GAGCAAAAGGCTTTGCAAGCATGTCATCTTCGACTGCCAATGAGAATATGTCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTTTACCACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

GAGCAAAAGGCTTTGCAAGCATGTCATCTTCGACTGCCAATGAGAATATGTCTACTGAAACTGGCACCCTGCCTCCCATGCCTCCCCCATCATCATACATgtgagttctc ... atctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTTTACCACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaagtttacctttgaatggatgaatgctaacttagcatataatctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTTTACCACG
                            tgctaac  putative branch site (score: 160)
                                              tctctgc  putative PPT
                                        atataatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctccctcttgtttctctgtctgctgtcattaagtttacctttgaatggatgaatgctaacttagcatataatctctgcagTGGTTCGCCTGTTTTCTGGATTGGAGTTGGTGTAGCATTGTCTGTGGCGTTTACCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG