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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaattatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT

Basic information

species Zea mays
transcript GRMZM2G138505_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
gttagtaatta-tttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
|| ||||| || | |||     || |||||| |||| |||  | |  |||||||||  ||||  |   | |  |    || || ||| ||||||| || |||||||||||  |||| ||||||||||| |||||||||||||| || |||||||||||||||||||| |||||||||   |||||||| |
gtcagtaaataatattttgaattgatatttagctttcttc--ttggtcccttgcttttctttcat--atgctttcactttcat-cttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT

upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G17110.1 (Glycine max), 3'ss of exon 8
gttagta-attatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
|| |||  |  | | |   ||||    ||||  ||       | | |  ||  ||  |       ||   || ||| || | |  |||||||| |||| ||||||||||| || || |||||  | ||  ||||||||||||| || ||||||||||||||||||||||  ||||||   ||| ||||||
gtcagtgcaccaatctgttctct----tttaaattgcaatgataggcatctatctcactcgcagctaactcatttg-gtgtgta-tttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGATAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCATTCAGAGCTCGGGATATTACAT

upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
gttagtaattatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
    || |  ||||| || |  || ||  |  | ||||   |  ||   ||     ||||    || |    || ||| |    ||||||||||||| |||||||| || || || |||||| | ||||||||||| ||||| ||| |||||||||| ||||  || || || |||   |||||||| |
----gtgag-attttgaatt--gtaatacagttcttttgttttaacttttt--cagccttcagctaattagcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT

upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G29670.1 (Glycine max), 3'ss of exon 8
gttagta-attatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
|| |||  |  | | |   ||||    ||||  ||       | | |   |  ||  |       ||   | ||| ||| | |  |||||||| |||| ||||||||||| || || ||||| || ||  ||||||||||||| || ||||||||||||||||| ||||  ||||||   ||| |||| |
gtcagtccaccaatctgttctct----tttaaattgcaatgataggcatttatctatctcacagctaactc-gttttgtgtgta-tttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGGTAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGATCATTCAGAGCTCGGGATATTACTT

upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G06790.4 (Glycine max), 3'ss of exon 7
gttagtaattatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
    || |  ||||  || |||  ||     ||||| |      | |  ||     |||||   || |    || ||| | |  ||||||||||||| |||||||| || || ||||||||| | ||||||||||||||||| ||| |||||||||| || |  ||||| || |||   |||||||| |
----gtgagaatttg-aattctaatacagttcttttgtt-----aacatttttcagcctttagctaattagcttttgtctctgatttagATGGTTGATCCTGGTGGCATTGCAAACTGGTCACTAACTCATGTTGATTGGTCTGAGAGAAAATGGCACCCTAAATCATACAGGGCTCAGGATGTTACTT

upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
gttagtaattatttttaactctgtt--------atttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
|| || ||||  |||| | |||           |  |   |  |||      ||    |   ||| |  | |   ||  ||    |  |||    ||||| |||| |||  ||| || ||||||||| | |||||  ||||||||||||| ||| |||| |||||||||||   ||| |   ||| |||| | ||  
gtgag-aattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC

upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT5G57270.2 (Arabidopsis thaliana), 3'ss of exon 8
gttagtaattatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattcttta--gATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
|| || |  |  |   |||| | |       |||||         | |  || |||   |   ||| |  | |    ||| ||| |||  |||| |||| ||||| |||||  | ||||||||||| ||  ||||||||||||| ||| | | ||||||||||| | ||||||||||    |||||  || 
gtgaggagattataacaactttctc-----tcttttaaaagctttcactgtgattcttgtcccttaatgaaatc---tttgttccttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC

upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
------gttagtaattatttttaactctgttat-ttaccttttttccctcgaccccttgcttcccttt--ttttagtacagtt------------gtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
        || |  ||  ||    ||   || | ||||| ||   || |  |   ||   || ||| |   || |  | | |              | | | |  || ||||| |||| || | ||||||||| |||||||| || || ||||| |||||||||||||| ||||||||||| | |   || |  ||   |||  | ||  
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC

upper sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S38_381V6.1 (Physcomitrella patens), 3'ss of exon 7
gttagtaattatttttaactctgttatttacctttt---ttccctc---gaccccttgcttccctttttttagtacagttgt-----gtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
| | ||| |  |||    |||| ||      |  ||   ||   |    || || | |       || || |   ||  |||      ||  |  || ||||| | ||  | |      |  | || ||| | ||||| |||||||||||||| ||||| ||||||||||| | ||| |||       | ||  | ||  
gcttgtattattttgcttctctcttgcgcgtcaattagattaggtttgggatccgtagtgatatattattgacagcatgtgtccgatattactagttcagATGATGGATGCGGCCCACCTTTCAAATTGGACTGTGACCCATGTTGATTGGTCAGAGGGTAAATGGCATCCTAAGTCTTATGAGAAGACTGACATCACGG

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|9254423|gb|BE344891.1|BE344891
EST:     AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
genomic: AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
EST: gi|211360336|gb|FL143959.1|FL143959
EST:     AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
genomic: AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
EST: gi|101387921|gb|EB815974.1|EB815974
EST:     AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
genomic: AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
EST: gi|71762140|gb|DR960077.1|DR960077
EST:     AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
genomic: AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
EST: gi|211360335|gb|FL143958.1|FL143958
EST:     AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
genomic: AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
EST: gi|71772236|gb|DR970173.1|DR970173
EST:     AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAAT                         ATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG
genomic: AAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGG

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), 49 (downstream exon)
Score: 90

CCAGCAGAAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 74

CCAGCAGAAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

CCAGCAGAAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 86

CCAGCAGAAGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCCTCTTCAATgttagtaatt ... tattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT
                                           tttattcttt  CT-rich tract
                        tttttttagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaattatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG