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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgtgaccaccagtatttttttacacttacaaactgttatgtcctgaagcatatttaacagtggcttttgctgtcttctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT

Basic information

species Zea mays
transcript GRMZM2G137707_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g46640.1 (Oryza sativa), 3'ss of exon 2
gtatgctgtgaccaccagt-atttt--tttacacttacaaac----tgttatgtcctgaagcatatttaacagtggcttttgctgtcttcttt-ttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
||||| ||  || |  ||| | | |  ||  || | | ||||      || || |||||| ||| | | ||| |  || ||  || |||| || |||||||||||||||||||| || || ||  | ||||||||||| |||||| | |||||||||||| | |||||||||||||||||||||||||||||
gtatgttg--actagaagttactataattggcattcataaacgttgctttgtgacctgaaacatgtgttacaattactgtttttgacttccttgttgcagTGGCTTGTTGAATACAACGCGGCACTAGCATCAGTCTGCTTTATGGTGCTTCTTGGATTTATTGATGATGTTCTTGATGTTCCATGGAGAGT

upper sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G34640.1 (Glycine max), 3'ss of exon 2
---------gtatgctgtgaccaccagtattt--ttttacacttacaaactgtta-tgtcctgaagcatatttaacagtggcttttgctgtcttctt---tttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
         || |   || |     |||||||  ||  || || | |   ||| | ||   | ||    |   |  ||    || ||   | || ||   ||||||||||||||||||||| ||||||||| | || |   ||||||| ||||   | || |||||||| || ||||| |||||||| |||||||||||
gtaagttatgtgtatggtaaatctgagtatttagttcaactctaatatcttgtaactgatatcaatagaagaaaggagcactttgtgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCGCTAGCGTGCATCTGTTTCATGACATTGCTAGGATTTGTTGACGATGTCCTTGATGTCCCATGGAGAGT

upper sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 2
---------gtatgctgtgaccaccagtattttttt--acacttacaaactg----ttatgtcctgaagcatatttaacagtggcttttgctgtcttct-ttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
         |  |   || |     ||||||| |||  || || | |   ||    | || ||   |     |   | || ||   |    | | ||   |||||||||||||||||||||| |||||||| || || |   | ||||| ||||  || || ||||||||||||||||| |||||||| |||||||||||
gtaagttatgagtatggtaaatctgagtatttgttttgactctaatatcttggaactgatatcaatagaagaaaggagcattgttatgaattatttttggttttgcagTGGCTTGTTGAATACAATGCAGCATTAGCGTGCATTTGTTTCATGACACTGCTAGGATTTGTCGATGATGTCCTTGATGTCCCATGGAGAGT

upper sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT2G41490.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgctgtgaccaccagtatttttttacacttacaaactgttatgtcctgaagcatatttaacagtggcttttgctgtcttctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
||| | ||||  ||  |   | || ||  | |||    ||||  |       |  ||   |    |||  | | ||||     | | ||||||||||||| || |||||||||||  | |||||  | || || |||||| | ||||||||||| |||||||| |||||||| || ||||||||
gtaag-tgtg--cattaacgtcttgtttta-ttaatctctgtggttattctcattatcaatgtttgtgagtctggctgatgattctgtgcagTGGCTTGTGGAGTATAATGCAGCACTAGCATCTATTTGCTTCATGATTTTGCTTGGATTTGTAGATGATGTCCTTGATGTGCCTTGGAGAGT

upper sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 2
------gtatgctgtgaccaccagtatttt--tttacacttacaaactgttatgtcctgaagcatatttaacagtggcttttgctgtcttctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
      ||  |||  | ||     || ||   | |    ||  | ||  ||   || |  | | | |  ||        ||  ||   |  ||  |||||||||||||||| || |||||||| || |||||  |||| || ||||  || ||||||||||| ||||||||||||||| |||||||||||||
atttaagttagctaagccctaggttagttaggtctgactttgaagacattttcttcttttaacttttagaattaaaatgttgactacttcattcatgcagTGGCTTGTTGAGTACAATGCAGCCTTAGCATCCATCTGCTTCATGACCCTGCTTGGATTTGTAGATGATGTTCTTGATATTCCATGGAGAGT

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|67012698|gb|CO441447.1|CO441447
EST:     CTATGCCCCANACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: CTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|71438733|gb|DR819783.1|DR819783
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|74232443|gb|DT640357.1|DT640357
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|50331152|gb|CO526278.1|CO526278
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAGTGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|50337237|gb|CO532363.1|CO532363
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|91874805|gb|EB404762.1|EB404762
EST:     GGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCCTGTTTTATGATTCT
genomic: GGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCC-AGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTC-TGTTTTATGATTCT
EST: gi|101388899|gb|EB816431.1|EB816431
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|149041344|gb|EE046982.2|EE046982
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|149078632|gb|EE167420.2|EE167420
EST:     GGTCATTGCTATTATATTTCAGCAGTTTTC-CTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: GGTCATTGCTATTATATTTCAGCAGTTT-CACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|149107025|gb|EE188920.2|EE188920
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|78122710|gb|DV541094.1|DV541094
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCACACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|78108109|gb|DV526527.1|DV526527
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
EST: gi|71442204|gb|DR823254.1|DR823254
EST:     TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATT                         TGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT
genomic: TGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTT

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), 41 (downstream exon)
Score: 118

GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 194

GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 166

GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 93

GCCTGAAGCACTAGGTCTTGTTGTGGGGATTATCTACTTGGTCATTGCTATTATATTTCAGCAGTTTCACTATGCCCCAGACTCCATTgtatgctgtg ... ctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgttatgtcctgaagcatatttaacagtggcttttgctgtcttctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT
                    atttaac  putative branch site (score: 93)
                                cttttgctgtcttctt  putative PPT
                  atatttaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgtgaccaccagtatttttttacacttacaaactgttatgtcctgaagcatatttaacagtggcttttgctgtcttctttttgcagTGGCTTGTTGAATATAATGCAGCGTTGGCATCAGTCTGTTTTATGATTCTTCTTGGATTTGTCGATGATGTTCTTGATGTTCCATGGAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA