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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcaactgcttttcaagtttgaacagatttgaatcttgtatgtttgataccttcattcacttcaatattgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT

Basic information

species Zea mays
transcript GRMZM2G023020_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g32670.1 (Oryza sativa), 3'ss of exon 3
-gtagcaactgcttttcaagtttgaacagatttgaat-------cttgtatgtttgataccttcattcacttcaatattgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT
  |||||| || |||| ||||   ||||||| |||||       ||| |   ||||   | |  | |||||||| |  ||| ||||||||| ||||||||||| |||||||| |||||||||| ||| ||  | || ||||||||||| || |||||| |||| |||||||||||||||||||| |||
gttagcaa-tgtttttaaagt---aacagatctgaatttttatccttctggttttgtcccatgtactcacttcagtgatgttatacagAGGGGCGCGAGCTTCCCTATGGGAAAACTTCAAGAACAATCCATTATTCGACATTTCCACGGATCACCCTCCCACCTACTATGAAGACATGCAGCGTGCT

upper sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------gtagcaactgcttttcaagtttgaacagatttgaatcttgtatgtttgataccttc--attcacttcaatattgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT
                   ||| || |    ||  |  |         |   |||   |   |||   | || |  | |        | |  |  || ||||||||  ||||  || | |||||||||||||||| ||||||| |||||||||| || ||||| |||||  | || ||||| |||||||||||| | || 
acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
















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|40336812|gb|CK370882.1|CK370882
EST:     GGACTTTTTTATGACACGGGGAATGACCCTGAGGGCGGATACTACGCAAG                         AGGTGCGCGAGCTTCTTTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
EST: gi|74237462|gb|DT645376.1|DT645376
EST:     GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
EST: gi|88752698|gb|DY536839.1|DY536839
EST:     CCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: CCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
EST: gi|76292971|gb|DV032539.1|DV032539
EST:     GACACGGGGAATGACCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
EST: gi|78179883|gb|DV550256.1|DV550256
EST:     GGACTTTTTTATGACACGGGGAATGACCCTGAGGGCGGATACTACGCAAG                         AGGTGCGCGAGCTTCTTTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
EST: gi|78117432|gb|DV535819.1|DV535819
EST:     CCCGAGGGCGGATTTTATGCAAG                         AGGTGCGGGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: CCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
EST: gi|61118962|gb|DN559923.1|DN559923
EST:     GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
EST: gi|74232586|gb|DT640500.1|DT640500
EST:     GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAG                         AGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA
genomic: GGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 106

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 135

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

CTCACTTGATTTCCCCAGACACTCCACGCTCAATCTTCGTTTACTTCCGGGGACTTTTTTATGACACGGGGAATGACCCCGAGGGCGGATACTATGCAAGgtagcaactg ... tgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagatttgaatcttgtatgtttgataccttcattcacttcaatattgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT
                  gtttgat  putative branch site (score: 184)
                                     ttcaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcaactgcttttcaagtttgaacagatttgaatcttgtatgtttgataccttcattcacttcaatattgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA