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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatttattgcgataaatttcttattttgttcttaagctttaaaccttgacttgagcaaatacatgagtc...

Basic information

species Zea mays
transcript GRMZM2G102858_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 10
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatttattgcgataaatttcttattttgttcttaagctttaaaccttgacttgagcaaatacatgagtc
|| ||||| ||||||||||||| ||| || || || |||||  |  | ||||| ||||| || || ||||||||||| |||||||| ||||||||||  | ||  |   |  ||        || ||||       | || | ||||              |||  |   |  ||  |    |    ||   |
GTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAGgttatttataaaatatttgaaccctagtcagtatttgcatttgtgaaatccttaagcaagctgacttttttgtaatgtagctctactggaagtctggaac

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 10
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatt--tattgcgataaatttc----ttattttgttctt--aagctttaaaccttgacttgagcaaat----acatgagtc------------------------------------------------------------------------
|||   || ||  | || || | ||| || || || || ||  |  | || |||||||| ||||||||||| ||||| || |||||||||||||||    |   | ||      | | | |  | | |   |   | | | || ||    ||| || ||   |  | | |||    | || || | | ||||    | ||  |                                                                          
GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttgcttaatttattattaacgaaatgacacaccaacatatgtcaacattaattcgtctgtgtaggtttttgtgcatgtctagtggaaattgaaatatatgcttgttatatgctattacttcttctattctcctaagtgcaacttcagaagtatctatatggaatgctggaacag

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 10
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatt--tattgcgataaatttc----ttattttgttctta--agctttaaaccttgacttgagcaaatacatgagtc---------------------------------------------------------------------
|||   || ||  | || || | ||| || || || || ||  |  | || |||||||| ||||||||||| ||||| || |||||||||||||||    |   ||||      | | | |  | | |  ||   | | | || ||    ||| || ||   |    | |||    | || |||||  | |||  |  |                                                                       
GTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAGgttcatctatttacttaatttattattaacgaaatgatacaccaacatatgtcaacattaattcgtctgtgtgggtttttgtgcatgtcttgaa-atatatgtttgctatatgctattaccttttctattctcccaagtgtaacttcagaagtatctatatggaatgtgtggaacag

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 10
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatttat-tgcgataaatttcttattttgttcttaagctttaaaccttgacttgagcaaatacatgagtc--
|||   |||||| | || || | ||| || ||||| |||||  |  | || |||||||| ||||||||||| |||||||| |||||||| ||||||    |     || | | || | | ||  || |  | | |  ||    | |     |||  ||  | |   |   ||  ||  | |   ||| ||| |   
GTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAGgttcatgtcttggct-taagaattattatttcagtattatacactatgcctatatgaatgtgtttgtgttggtatgttt--ctgtatcttctacttgaatttc

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatttattgcgataaatttcttattttgttcttaagctttaaaccttgacttgagcaaatacatgagtc
|||  ||| ||| | ||||||| ||| || ||| | |||||  |  | ||||||||||| ||||| ||||| |||||||||||| ||||||||||| | | ||| | | | | || | ||  |   |   |  | ||    || ||| | | |  |||  |  ||  | || |   |                
GTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAGgtttg-tctagaatttttacaactttagaaaagtcagtgtctat---cttgttagtgt-taattagtcgctattcattaatccgcag-------------

upper sequence: GRMZM2G102858_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 11
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatttattgcgataa-atttct---tattttgttcttaagctttaaaccttgacttgagcaaatacatgagtc
||||  || ||  | ||||| | ||| |||||| | |||||  |  |||||||||||||||| || ||||| ||||| || |||||||| |||||     | | |||     |   || | | | |  | ||     |  |||  |   ||| ||| | || | | |  |      |  ||   ||    |  ||  
GTTTATTCAATTCGTGATGCAGCTGCTAATAATGTGAAGCGCCTTGCAGAGGAATTTGGCCCAGATTGGGCAATGCAGCACATAATTCCACAGgtctttctgattacatattactgtgaattggtaccttttaaacaagcattgataaatatcttgctgttcaacat--agatacaaagtgtctaatctgacaag--

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|60354743|gb|DN221716.1|DN221716
EST:     TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|149079804|gb|EE168801.2|EE168801
EST:     NGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|4681251|gb|AI629921.1|AI629921
EST:     AATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: AATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|18661338|gb|BM501361.1|BM501361
EST:     GGGCGATGCAACATATAATTCCCCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: GGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|50336585|gb|CO531711.1|CO531711
EST:     TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|7227754|gb|AW566395.1|AW566395
EST:     TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCCCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|60399443|gb|DN232255.1|DN232255
EST:     TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|50336586|gb|CO531712.1|CO531712
EST:     TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|113672925|gb|DW825465.1|DW825465
EST:     GCGATGCAACATATAATTCCTCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: GCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|40303113|gb|CK347500.1|CK347500
EST:     TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCCCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|6194513|gb|AW146617.1|AW146617
EST:     TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCCCAG                         GTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG
EST: gi|32851132|gb|CD990813.1|CD990813
EST:     TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCCCAG                         GTTTTGGAGAAGA-AAACAACCCA-ATTATCTGTATCGGATGACCACTTTG
genomic: TGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTG

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), 47 (downstream exon)
Score: 223

GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 151

GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCC


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 154

GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 163

GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagcttta ... tatattctagGTTTTGGAGAAGATAAACAACCCACATTATCTGTATCGGATGACCACTTTGCAAGCTATTTCTTTGCTAGCTCCTGTCATGGGTCCTGATATCACATGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAGgttagctttagtactgtgaaaaatgtaatagcatttattgcgataaatttcttattttgttcttaagctttaaaccttgacttgagcaaatacatgagtc

- - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaatg