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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattggacggttgatctttttaggttctgttgcgcctgtcttctccatatccttttgaaagtttggataccatttccccccctcgacttctaactctctgcaactgcacaatgttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT

Basic information

species Zea mays
transcript GRMZM2G035985_T01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035985_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os07g46370.1 (Oryza sativa), 3'ss of exon 21
gtagattggacggttgatctttttaggttctgttgcgc-ctgtcttctccatatccttttgaaagtttggataccatttccccccctcgacttctaactctctgcaactgcacaatgttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCT-TGT
              |||  ||     ||  | || ||| ||||    |  |||   |  |||      | |||   |||     | |    | |||| | |     ||||  |||||||||   ||||||||  | || || |||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||||||   || 
--------------tgacgtt----agtcattttccgcactgtggatttgatagattgctga------gtataattttttattgctttttatcctaattattaattactgttcaatgttgg---cagGTACTTCTGACAACGAGCGACTGGGACGAGTGCAACTTCTGGCTTGCCGCATTGAAGCGTATGATCAAGACGAGGCAGAATTTCAGAATGTAAACGAGTG-

upper sequence: GRMZM2G035985_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA12G01290.1 (Glycine max), 3'ss of exon 21
gtagattggacggttgatctttttaggttctgttgcgcctgtcttctccatatccttttgaaagtttggataccatttccccccctcgacttctaactctctgcaactgcacaatgttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATG---TAAACCTTGT
                       ||  | |  ||||   ||     |  |||   |||   |  | || | |  | | |  |   || || |   |  ||||     |      |||||    ||||| ||  | || || |  || |||||||| ||| | | |||| | |   || | |||||||||||||||||||||||||     ||| |    ||||      
----------------------gtaaat-caattgcaaatgcaaatt--atagtattt---acctgtgtaaaaaactccatcaaatctacattctagcctctttttttttttcgtgttg----cagGTTCTTCTTACTACTACTGAGTGGGACGAATGCCAATCCTGGTTAGGTTCACTCAAGCGGATGATCAAGACAAGGCAGAGCGCGAGACTAGGTTAAAAAA---

upper sequence: GRMZM2G035985_T01 (Zea mays), 3'ss of exon 21
lower sequence: Vv13s0158g00140.t01 (Vitis vinifera), 3'ss of exon 21
gtagattggacggttgatctttttaggttctgttgcgcctgtcttctccatatccttttgaaagtttggataccatttccccccctcgacttctaactctctgcaactgcacaatgttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT---
                || ||| | ||   |           |||   ||  |||   ||| |  |   ||   ||||   |        || | | |||                 ||| |  |||||||  | ||||| || || ||||| ||||||||||||||||| ||  || | ||| ||||||||||||||||||||||| | ||| |   ||  | |    
--------------gtatatttctggggattaaaatattcaacttaggcaactccaaatgagaaatgacattgtatttggtctt------tttttattcttc--------------ctgg-gatagGTACTTCTTACGACCAGTGAGTGGGATGAGTGCAACTTCTGGCTAGCAACACTAAAGAGGATGATCAAGACAAGGCAGAATGTGAGATT---AAGTTAGAGAG

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|5325046|gb|AI783237.1|AI783237
EST:     TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAG                         GTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
genomic: TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
EST: gi|16921694|gb|BM075249.1|BM075249
EST:     TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAG                         GTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
genomic: TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
EST: gi|5152776|gb|AI759074.1|AI759074
EST:     TGTGCAGTGCGATTGATGCTAGCGATTTTGTCCCCGCGATGCACCTCCAG                         GTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
genomic: TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
EST: gi|18164811|gb|BM334650.1|BM334650
EST:     TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAG                         GTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
genomic: TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
EST: gi|6031275|gb|AW076282.1|AW076282
EST:     TGTGCAGTGCGATTGATGCGAGCGATTTTGTCACCGCGATGCACCTCCAG                         GTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
genomic: TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
EST: gi|6031264|gb|AW076271.1|AW076271
EST:     TGTGCAGTGCGATTGATGCGGGCGATTTTGTCACCGCGATGCACCTCCAG                         GTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
genomic: TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
EST: gi|5846858|gb|AI999941.1|AI999941
EST:     TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAG                         GTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA
genomic: TGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCA

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), 49 (downstream exon)
Score: 188

ACTAAATAGTGGTGACATATCTCCAAACGTTTCATCAAAACTCATTCAGCTGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

ACTAAATAGTGGTGACATATCTCCAAACGTTTCATCAAAACTCATTCAGCTGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

ACTAAATAGTGGTGACATATCTCCAAACGTTTCATCAAAACTCATTCAGCTGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

ACTAAATAGTGGTGACATATCTCCAAACGTTTCATCAAAACTCATTCAGCTGTGCAGTGCGATTGATGCTAGCGATTTTGTCACCGCGATGCACCTCCAGgtagattgga ... ttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatttccccccctcgacttctaactctctgcaactgcacaatgttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT
                   ttctaac  putative branch site (score: 156)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattggacggttgatctttttaggttctgttgcgcctgtcttctccatatccttttgaaagtttggataccatttccccccctcgacttctaactctctgcaactgcacaatgttggtgtcagGTACTCTTAACGACAAGCGACTGGGACGAGTGCAACTTCTGGCTTGCGGCATTGAAGCGGATGATCAAGACAAGGCAGAATTTCAGAATGTAAACCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC