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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattgacatccgctgacccacacacaaagtggccaatttacctttattttctatttttttcttaatgacaccagtttctttgttttgtatttgttttttaaatctttgataaatgacaattcttgtttag

Basic information

species Zea mays
transcript GRMZM2G386991_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 10
GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattgacatccgctgaccca-------cacacaaagtggccaatttacctttatt-ttctatttttttcttaatgacaccagtttctttgttttgtatttgttttttaaatctttgataaatgacaattcttgtttag
||||||||||||||||||||||| |||||||| |||||   ||||||||||||||||||||| || ||||| ||||||||||| || ||||||||||||||||| |    |||   ||   |||       |  | |||||||   |  ||  | ||||  | | |||| ||  |  | ||    ||||  || |||  | | | | |||| | |    |                      
GCTATCAAGCTGATTGATTTTGGAAGTACAACATTCGAACACCAAGACCACAATTATGTGGTATCAACAAGGCATTATCGTGCCCCTGAAGTTATCCTTGgtattaacatcatatccttttccatttcccccctataaagtggaacacataattatattactgtgttttgtttatggt-acctttgtttagttatttcctttctctgttttcatttgcag----------------------

upper sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G33100.1 (Glycine max), 5'ss of exon 8
GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattgacatccgctgacccacacacaaagtggccaatttacctttattttctatttttttcttaatgacaccagtttctttgttttgtatttgttttttaaatctttgataaatgacaattcttgtttag
|| || ||||| |||||||| ||||||||| | || ||    || || |||| |||||| || || |||||||| ||||||||||||||||||||| | ||||  |||| ||| |  |||     |  |        |||||   ||||||     |    | |   | |  ||  |  || || ||||  | ||| |  | ||                              
GCCATTAAGCTCATTGATTTCGGGAGTACATCATTTGAACATCAGGATCACAGTTATGTTGTTTCAACAAGACACTATCGTGCACCAGAAGTTATCTTAGgta--attgtcattccttgaaatgtatgc-------tcaattgctctttat-----acccatgttccagt--cattatatttttcgtttgttgttt-tcctgtag-----------------------------

upper sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT3G53570.2 (Arabidopsis thaliana), 5'ss of exon 9
GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtata-attgacatccgctgacccacacacaaagtggccaatttacctttattttctatttttttcttaatgacaccagtttctttgttttgtatttgttttttaaatctttgataaatgacaattcttgtttag
|| |||||||| |||||||| || |||||||| || ||    |||||||| || ||  | || || ||||||||||| || ||||||||||||||||| |||| |  || |   |  ||||| ||   ||   || |   ||| |  ||| | |    |  |  | || | ||     |    ||| ||                                              
GCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATCAAGACCATAACTACATTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAGgtaaacgtttatgact-ctgacacatctac---gtagatgatt-atttttttgtgtagtcatggtatttaagagtttggaacgtttattgcag------------------------------------------

upper sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0040g02640.t01 (Vitis vinifera), 5'ss of exon 8
GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattgacatccgctgacccacacacaaagtggccaatttacctttattttctatttttttcttaatgacaccagtttctttgttttgtatttgttttttaaatctttgataaatgacaattcttgtttag
|| || ||||| |||||||||||||||||||| || ||   ||| || ||||| ||||||||||| ||||||||||| ||||||||||| |||||  | ||||  ||||  | |  |   ||   | ||   || |    | |   |||  | |  ||  |||   | |||| |     |||| | |  || |                                         
GCCATTAAGCTCATTGATTTTGGGAGTACAACATTTGAACACCAGGATCACAACTATGTGGTGTCAACAAGACATTACCGTGCACCAGAGGTTATTTTGGgta--attgttaactcc---ccattagactcggtagttggtat---tttgatattaatagtttagatgatga-atattgttctgtttactgcag----------------------------------------

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|211512137|gb|FL430403.1|FL430403
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|211073306|gb|FL473576.1|FL473576
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|19822133|gb|BQ048157.1|BQ048157
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|19769965|gb|BQ034686.1|BQ034686
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|31997648|gb|CD661693.1|CD661693
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|211122243|gb|FL474055.1|FL474055
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|211212596|gb|FL411382.1|FL411382
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|19822056|gb|BQ048080.1|BQ048080
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|15426933|gb|BI542755.1|BI542755
EST:     TTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: TTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|15352988|gb|BI502599.1|BI502599
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|14245195|gb|BG873777.1|BG873777
EST:     AATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: AATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|60343108|gb|DN210081.1|DN210081
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|60354602|gb|DN221575.1|DN221575
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|6095292|gb|AW119959.1|AW119959
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|45847998|gb|CN071941.1|CN071941
EST:     CAATTATGTGGTGTCGACCAGACATTATCGTGCCCCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAG
EST: gi|6695913|gb|AW289021.1|AW289021
EST:     CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTG                         GTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTT
genomic: CAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTT

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: 48 (upstream exon), 47 (downstream exon)
Score: 134

GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 118

GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 120

GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattga ... tcttgtttagGTCTTGGGTGGAACTATCCATGCGACTTGTGGAGTGTGGGTTGCATTTTAGTTGAGCTTTGTTCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtataattgacatccgctgacccacacacaaagtggccaatttacctttattttctatttttttcttaatgacaccagtttctttgttttgtatttgttttttaaatctttgataaatgacaattcttgtttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT