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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcctgtgctttacagacaaacgttttcccagctccacaattgtcatcgactctttagcctgctcacctgttcaggaagcaacttcgacctgtgatgctgtatcttttgcttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC

Basic information

species Zea mays
transcript AC189879.3_FGT003
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
gtatgtcctgtgctttacagacaaacgttttcccagctccacaattgtcatcgactctttagcctgctcacctgttcaggaagcaacttcgacctgtga-tgctgtatcttttgcttctt-----aacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGAC---GTCGAAGAGCTCCAATGGCAC
||| || ||         |    ||| |||| ||| |       |||| ||  |    |||      | |   |||  |||  | | |||     |||| |  || || | ||  ||| |     |||||| || ||||||||||| || || ||||| || || || ||||||||||||||||| |||||||||||||||||||||||   |||||||||||||| |||   
gtacgttcttctgaaatgatctgaacatttttccatcattttctttgt-attcatgtgtta------ttattagtt--ggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG---

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 20
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 19
gtatgtcctgtgctttacagacaaacgttttcccagctccacaattgtcatcgactctttagcctgctcacctgttcaggaagcaacttcgacctgtgatgctgtatcttttgcttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC
                                                  |  |  |  ||||    || | |   |    | |||||    |         |   || ||| |||     |||| || |||||||||||||| |||||||| || ||||| ||| | ||||||||||| || ||   ||| |||       |     |  |   || ||   |
-------------------------------------------------gtaaagaccatagctctttcccataggctttga-caactaaagcacaaagcaat-cgtccttttcttt----cagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGGCTGGCTCCGTCCACCGGAACACTGCTCC

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 20
lower sequence: EFJ14096 (Selaginella moellendorffii), 3'ss of exon 19
gtatgtcctgtgctttacagacaaacgttttcccagctccacaattgtcatcgactctttagcctgctcacctgttcaggaagcaacttcgacctgtgatgctgtatcttttgcttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC
                                                  |  |  |  ||||    || | |   |    | |||||    |         |   |||||| |||     |||| || |||||||||||||| |||||||| || ||||| ||| | ||||||||||| || ||   ||| |||       |     |  |   || ||   |
-------------------------------------------------gtaaagaccatagctctttcccataggctttga-caactaaagcacaaagcaat-cgtctttttcttt----cagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGGCTGGCTCCGTCCACCGGAACACTGCTCC

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|166622653|gb|EG304138.1|EG304138
EST:     TTATGCCCGGTGCACACGCTCGGTTTCTGTTG                         TCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACA
genomic: TTATGCCCGGTGCACACGCTCGGTTTCTGTTGgtatgtcctg ... ttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACA
EST: gi|19351412|gb|BM895959.1|BM895959
EST:     TTATGCCCGGTGCACACGCTCGGTTTCTGTTG                         TCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGCTTCTACA
genomic: TTATGCCCGGTGCACACGCTCGGTTTCTGTTGgtatgtcctg ... ttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACA

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: 32 (upstream exon), 49 (downstream exon)
Score: 505

TTATGCCCGGTGCACACGCTCGGTTTCTGTTGgtatgtcctg ... ttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 108

TTATGCCCGGTGCACACGCTCGGTTTCTGTTGgtatgtcctg ... ttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 53

TTATGCCCGGTGCACACGCTCGGTTTCTGTTGgtatgtcctg ... ttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC


Block sizes: 32 (upstream exon), 44 (downstream exon)
Score: 66

TTATGCCCGGTGCACACGCTCGGTTTCTGTTGgtatgtcctg ... ttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgttcaggaagcaacttcgacctgtgatgctgtatcttttgcttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC
 tgctcac  putative branch site (score: 66)
                                   tatcttttgcttctt  putative PPT
                                   tatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcctgtgctttacagacaaacgttttcccagctccacaattgtcatcgactctttagcctgctcacctgttcaggaagcaacttcgacctgtgatgctgtatcttttgcttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT