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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgtt-gcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
|||  | |||||||  |||  || |||   |||  |||     ||| ||| | ||||||  | || |||    |||| |||| | ||     | ||||||  ||  | |         |  | | ||||||| ||||||||| |||||||||||||| ||||||||||||||||| ||||| || ||||||||||| ||||||||||||||
gttaggattttgct--ctgggatatttcataatagaattg---aaacatcttgtttccaattcagagttctttatttcttttttata-----tattagtttcgatcaaa---------agttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG

upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagtt--ctgagaacactatcgttga-actttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
||       |   ||| | |||| |||| |   |   || | |  |||   |  ||   ||| | | ||||    ||||   | || |  | ||| | ||   | |         | |||  ||||  |  | |  |||||||| || || |||||  ||||||| || |||||||| ||||| || || || |||||||| |||||||||||
gtcagttagtatatagttcttatattttgatggt---tatggatcatacttttgtttgtgctgatgctttc---attttggagattgacttctttgaattaattaatcttttcgacattggtacttattaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG

upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 2
gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagtt--ctgagaacactatcgttga-actttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
           |  || |  ||| |   |   ||  |||       |    | | |     ||   | || |   ||||   | || |  | ||| | ||   | |  |   |  | | |  |||   |  | |  |||||||| || || |||||  ||||||| || |||||||| ||||| || || || |||||||| |||||||||||
-----------gtcagttagtatatagctctgtttcatacttctgtttagttctgtttgtgttgatgctttc--attttggagattgacttctttgaattaattaatcattttgacatgggtactgattaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG

upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
gttgtgcttttgctagctgttattttttta-aattcaataagaaaaat---atcctatttccagcttagggtttcccattttttttgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
                  |||| ||| |    |  | || || ||| |   ||  || || || |  | |   ||  || ||| |    |    ||| ||  ||||             |   | || |||      ||||| || || |||||||| ||| ||||||| || ||||| ||||||||||| || ||||||||||||||||||||
------------------gttagtttctggtgacccgatgagtaaattggcattgtaatttcaccacaagaaatctgatgtttatgcacttgcctgtgttgattct-------------tctcatttcatgaa---acagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG

upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
||| || | |   ||  |     || || || |||||       |||||  | ||||| | || |    | |   ||| | | || |   | ||   |||||     |   ||| || |      || | |  |||||||| || ||||||||||||||||||||||| || || |||||||| ||||| |||||||| |||||||||||
gtt-tgttatgcttaattaaaggttattgaatttcaa-----gtaatattttttttcctgtttggaaaatacttgtttatctattcagcct-ttcctgttct-----cttgatcatttact----tgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG

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|71433814|gb|DR814864.1|DR814864
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|76924992|gb|DV170232.1|DV170232
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|148945041|gb|EC890225.2|EC890225
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|149003162|gb|EE038900.2|EE038900
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|211035971|gb|FL104471.1|FL104471
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|211038407|gb|FL104474.1|FL104474
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|149028361|gb|EE286119.2|EE286119
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|88758154|gb|DY542295.1|DY542295
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|211038406|gb|FL104473.1|FL104473
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAA-CAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|116827363|gb|EC871258.1|EC871258
EST:     AATCAACGTAACATCGCGAAATGGAGAAAACAGGAACGGGACAAG                         ATAGACGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTT
EST: gi|211038408|gb|FL104475.1|FL104475
EST:     AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAG                         ATAGAGGTTGGTGATGTGATATNGTGAGATAGAAACTGATAAAGCCACTCT
genomic: AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATAT-GTGAGATAGAAACTGATAAAGCCACTCT

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: 45 (upstream exon), 49 (downstream exon)
Score: 252

AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 351

AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 230

AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 492

AATCAAGGTAACATCGCGAAATGGAGAAAACAGGAAGGGGACAAGgttgtgcttt ... gttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
 gtttaat  putative branch site (score: 492)
           ttttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG