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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattatattcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg...

Basic information

species Zea mays
transcript GRMZM2G008327_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 5'ss of exon 1
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattatattcccccttttgcattgctgttatta--cgacggatttagggtc-gatcgatcggccgacgcatccgcg
||||||||||||| || ||||||||||| ||||||||||| |||||||| |||||||||||||| ||||||||||||||| | ||||||||||||||||||||| ||       | ||    |  |   |||          ||  |   |   | |      ||  ||||    | | ||| ||| | | ||   ||     
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGCGTCCCCTCCACCGCAATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACGGCAACATCGTCAGgtcctctctattaacactctgttgtt--gttaggactttggattgactaagtcatcacggactgattgattggttgcctgattgattgactgattgattgat-

upper sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g01850.1 (Oryza sativa), 5'ss of exon 3
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattat-attcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg--
||||||||||||| || ||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||||||||||||| | ||| ||||||||||||||||| ||       | |  |||||  |   | |  ||      |||| ||| |  |||||| || | | | |     ||  ||| |    |   ||    |  
TCAAGAAGATCCGGCTTGAGCAGGAGGATGAGGGTGTCCCCTCCACCGCCATCCGCGAGATCTCGCTCCTCAAGGAGATGCATCACCGCAACATCGTCAGgtcctctctattaac-caaccctctgctgctcttgtttaggactttggatt-cacttattagga-gtagtcatcacggactgattgattcattgattgatgtg

upper sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattatattcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg----
| |||||||| ||||||||||||||||| ||||| || ||   ||||||||| |||||||| |||||| | || || ||| | ||| | ||||| || ||||          |     |      |   ||    | |   | |   |||  |||  | |  | | || |    | ||   |  ||  ||              
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaa----tgtgttggtcttcaattgtgcaattcatgtgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag

upper sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattatattcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg-----
|||||||||| |||||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||||||||| |||||| | ||  | ||||| || ||||        |    ||   |  | | ||||  | | |      ||  ||| |||   |        |  |||||  ||      | || ||||  |        
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcat-ctaattccttctcctttcattggaatgca----atgtgttgttgtcgatgatgaaattggagggttaataatgttgtcgccgcactctatttgtc

upper sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 2
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccatt-atattcccccttttgc-attgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg
| |||||||| |||||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||| ||||| |||||| | ||  | ||||| || ||||        | |   |   |  | | ||||   || |    | |||   | | || |   |  |  | ||||     |  | ||  | ||  | ||  |  
TGAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatccatttcccttctcctttcatttgaatgcaatgtgttgttgtcgatgatgaaattaatgttttatccgtgcgctatttgtcg-tgaatttgt-

upper sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ15022 (Selaginella moellendorffii), 5'ss of exon 2
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattatattcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg
||||||||||||| || || ||||||||||||||||||||   ||| || |||||||| || || ||||||||||| ||| | ||||||||||| || |||| ||            || || | ||||||         || | | || |   ||  ||  ||| ||   |  | |   |  | |              
TCAAGAAGATCCGACTGGACCAGGAGGACGAGGGCGTCCCCAGCACGGCGATCCGCGAAATATCGCTCCTCAAGGAAATGCAGCACGGCAACATTGTGAGgtgcg------------tgtccacttccatt---------ctctggaatgg--atttctaaaacgaatc--gattgggctgcccag--------------

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|17921690|gb|BM259341.1|BM259341
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
EST: gi|87152029|gb|DY396818.1|DY396818
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
EST: gi|31362736|gb|CD447093.1|CD447093
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
EST: gi|7216555|gb|AW562677.1|AW562677
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGNCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
EST: gi|6095562|gb|AW120229.1|AW120229
EST:     ATCCGCGAGATCTCTCTCCTGAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
EST: gi|22489528|gb|BU049451.1|BU049451
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
EST: gi|61118496|gb|DN559457.1|DN559457
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
EST: gi|22542942|gb|BU093380.1|BU093380
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACC
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACC
EST: gi|93281356|gb|EB673620.1|EB673620
EST:     ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAG                         ATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA
genomic: ATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTA

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: 143

TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCCTGCCCGGAGTTTGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCCTGCCCGGAGTTTGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 37

TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCCTGCCCGGAGTTTGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 55

TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcg ... ctgcgtgcagATTACATGATGTTGTCCACAGCGAGAAGCGCATATACCTTGTCTTCGAGTACCTGGATCTGGACCTCAAGAAGTTCATGGACTCCTGCCCGGAGTTTGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccattatattcccccttttgcattgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcctcc