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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattca-tagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
|||||||    |||||||||||||| ||| |   |||            ||| ||    | || ||| ||||   | || ||||      ||||||| |||||  ||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||||||||||| ||||||||||| || || || || ||||||
gtagttaac--tactcctgatgttgatatgtgcgaag-----------caattttg---tccttaacgtggcgcaccttaatatcg----ttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattca-tagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
|||||||    ||| |||||||||| ||| |   |||            ||| ||    | || ||| ||||   | || ||||      ||||||| |||||  ||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||||||||||| ||||||||||| || || || || ||||||
gtagttaac--tacacctgatgttgatatgtgcgaag-----------caattttg---tccttaacgtggcgcaccttaatatcg----ttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 20
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatatt-catagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
||| ||  |  |  |      ||    ||  | | || |  |         |  |  | || |     |  ||   ||||  |||   |||  | | | ||  | ||||||||||| ||||| || ||||| ||||| || || ||||| | ||||||||| || || || || ||||||||||| ||||| || || || ||||||
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttt--tttttcaattattgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
gtagttactct-tactcctgatgttggtatttctta-----aggtggcatacctta-atattaaatttctcaacatggcatgcattgatattaaattttctttatattc---atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
||| || ||   |  |  |     || | |  ||       | |||       ||  | |    || |      ||  |||    | |||||   ||  |  || | |    | ||||||||||| || || || || || ||||| |||||||||||||  |||||||| |||||||| ||||||||||| || ||||| || | ||||||||||
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 20
gtagttactcttactcctgatg-----ttggtatttcttaaggtggcataccttaat--attaa---atttctcaacatggcatgcattgatattaaattttctttatattc----atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
||| || || | | |    |        | || |||||   |||   | |||| | |  ||| |   |||   |||  |    |    |||| |    |  |||  ||| |     | ||||||||||| ||||| || || || ||||| || ||||| ||||  ||||| || ||||| || ||||||||||| || ||||| || ||||||||||||
gtaatt-ctttcatttggaaaaaaaaacttgtttttctgttggtaatagacctcatttaattgagatattatccaatgta-tttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGATATTCACTTTAAGTACATTGAGGCAGCGGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
gtagttactcttactcctgatg----ttggtatttcttaaggtggcataccttaat--attaa---atttctcaacatggcatgcattgatattaaattttctttatattc----atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
||| || || | | |    |       | || |||||   |||     |||| | |  ||| |   |||   | |  |    |    |||| |    |  |||  ||| |     | ||||||||||| || || || || || ||||| || ||||| ||||  ||||| || ||||| || ||||||||||| || ||||| || ||||||||||||
gtaatt-ctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgta-tttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 19
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaat--------tttctttatattc---atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
   || ||||||  || || | || | | |  ||  | |||   ||      ||  ||||| | ||   |  ||    || ||| |  |        ||||  |  | |    | ||||||||||| || || || ||||| ||||| || ||||| ||||  |||||||| |||||||| ||||||||||| || ||||| || | ||| ||||||
---gtaactctt--tcatgtttttagaactgttttggctggtggacaagtg-atgcaatttgtaaaggggatattgtctgctatcagctaatatttttttccctgaacttgggacagTGAGGATCCTGACATTCACTTCAAGTACATTGAGGCAGCAGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTTTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 18
gtagttactct----tactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
||| ||  |       | |    |||     | ||||  |       ||      |   |  | | |  || |  |     |||   ||  ||| | | |   |  | ||||||||||| ||||| || ||||| || || ||||||||||| | ||||||||| || || || || |||||||| ||  | || || || || ||||||
gtatttcttaagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtct---tgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatat-taaatttctcaacatggcatgcattgatattaaat-tttctttatattc-atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
                 |||| | | ||     | |  | |  |   | || |   |   ||||     |   |||| |   | |  ||| ||||| | | | | ||||||||||||| || ||||||||||| ||||| ||||||||||| |  ||||| || || || || |||||||||||||| ||||||||||| |||||||||
----------------gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
gtagttac-tcttactcctgatgttggtatttctta-aggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
||| ||   ||    ||||| |||   |  |    | | |   ||| |   ||| ||  |||| |    ||| | | || ||        ||  || | | |  ||||||||||||| || || || ||||| ||||| ||||||||||| |  ||||| || || || || ||||||||||| || ||||||||||| || ||||||
gtaattttatcaagatcctgctgtcattcctgtaaacaagcaccatgcagcaat-ttgtattttt----atgacttacaatgtc------ttccctctgtgtg-atagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaat-ttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
                 |  |  |  || |     |     |  || ||||| ||||   || |    ||   ||    | || ||  |  ||| || |    | || ||||| || |||||||| ||||||||||| || |||||||| | ||||||||| || || || || || ||||| ||  | || || || || ||||||
----------------gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtat---attttcttatttttcaccttcattttgag-acagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT

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|32928656|gb|CF033468.1|CF033468
EST:     AAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAG                         TGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGG
genomic: AAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGG
EST: gi|32929052|gb|CF033864.1|CF033864
EST:     AAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAG                         TGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGG
genomic: AAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGG

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: 46 (upstream exon), 49 (downstream exon)
Score: 212

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 95

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 68

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 264

ATTCTGAACAACTAGGAGTTGATGCTTGCATAAAATTATTTGAACAATTCAAATCTTATGAGGGCCTCTACTTTTTCTTGGGATCCTATTTGAGCTCCAGgtagttactc ... atattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaaatttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
                        cattgat  putative branch site (score: 264)
                                     ttttctttatattc  putative PPT
                         attgatattaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaatttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT