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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

Basic information

species Zea mays
transcript GRMZM2G451882_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
tggctctcttgcttgtttggcgttttat--tttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctcta-----tctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
||||| |||| | || | ||| | | | | ||| | | | | |||| || | | | | | || | | ||||||||||||||||||||| |||||| ||||||||||||||||||| ||||||||||||||||||||||||||||||||
------ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttct-gtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 2
tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattc-tagttgtaaataatctctctat-ctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
| | | | || | ||| |||| | |||| || | | |||| | ||| | | || | | || | | |||||||| ||||||||||| | ||| |||| |||||||||| || || ||||||||||| || ||||||||||||||
--tgttattagggtattaacactaatatgttaatctgttaaagcttaatttgctgatcaatgcatttgttgtttttcttcatttattcataccaatttgcagTGTAATTGTTGAAGCCCTGAAGGTGGACAGTCTGCAGAAACTTTGTTCATCACTGGAGCCTATTCTTCGTAGAGTT

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
---tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccct--gcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
|| | | || ||| || || || || | | || | | | || | || | ||| | | ||| | || | | ||| | ||||||| ||||| |||||| | ||| |||| ||| |||||| ||| |||||||| | ||||| ||||||||||||||
atagggttttatttcttattaa---ttataattcatc-tagttgtttctaatttat-atttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
--tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
| | || || || | || | | | || | | | || | || | ||| | | ||| | || | | || |||||||| ||||| |||||| | ||| |||| ||| |||||| ||| |||||||| | ||||| ||||||||||||||
aaagaagattttatttcttattaatcataatccatc-tacttgtttctaatttat-atttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------tggctctcttgcttgtttggcgttttattttaa--cgtattaataacaaaataatgacctatcacatt--ctagttgtaaat------aatctctctatctacc-ctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
| ||| | | | || |||| | |||| ||| | |||| | | ||| | ||| || || | | ||| | |||||||| ||||| ||||| || |||||||||||| | |||||||| || || || ||||||| |||||||| ||||
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtggatttgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
tggctctcttgcttgtttggcgt---tttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
| ||||| ||||| | | | | ||||| | ||| | | | || ||| || | | || ||| | ||| || | |||||||| || || |||||| | ||| ||||||||||||||| || |||||||| ||||||| ||||||||||||||
-tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatt-tttatgtcagttctaatatag-taaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT

upper sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 1
------tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaata-atgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
| || | || || |||| | ||| |||| | | | ||| ||| | ||| | |||| | | | | | | |||||||| || ||||||||| | ||| ||||||||||||||| || ||||||||| ||||||| |||||||| |||||
caaacaaaggaatcgaggcagtg-ggttttttgtattatta-attagttccgttttctatgccctgtt--attttgtttgt---tgaaatgtacttttgttttgcagTGTAATAGTTGAAGCTCTGAAGGTGGATAGTCTGCAGAAACTTTGCTCATCATTGGAACCTATTCTTCGGAGAGTT

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|211076796|gb|FL055833.1|FL055833
EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|148941980|gb|EC886967.2|EC886967
EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211079522|gb|FL055834.1|FL055834
EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|149013593|gb|EE043063.2|EE043063
EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|211076795|gb|FL055832.1|FL055832
EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
EST: gi|71771244|gb|DR969181.1|DR969181
EST:     GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAG                         TGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC
genomic: GGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATC

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), 49 (downstream exon)
Score: 267

TGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 189

TGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 223

TGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 162

TGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGGCCTCCGGCACTGGCCAGgtgaggaatt ... taccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
                                   tctctctatctaccct  CT-rich tract
 tagttgtaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacattc