Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcacatgatttcccttgtatccagtgtgtacgcatgtttgtttatgcttatgcatttcatttaatgaaccctgatgtatgttaaaatgaatttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACCATAGACTTG

Basic information

species Zea mays
transcript GRMZM2G110289_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110289_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g13050.1 (Oryza sativa), 3'ss of exon 11
-ctcacatgatttcccttgtatccagtgtgtacg-catgtttgtttatgcttatgcatttcatttaatgaaccctgatgtatgttaaaatgaatttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACCATAGACTTG
   |||||   |    || | |  | | |||  | ||| |||    | |       ||||  |||  |      | |  ||  |||| |||||| |||||||||||||||||||||||| || ||||||||| | || ||||||||||||||  ||||||||
gtacacatttatgtaattatgtttactttgtttggcatttttagagaaggaaggtgattttgtttggtt--ttgtaacataaattaatatgaatgtcaccagGGAGCTGAAAAGGTTGCAGATGCTCTGAAACAGAATAAAACAATTTCTACTGTAGACTTG
















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|15208880|gb|BI430764.1|BI430764
EST:     AAAGTCCTTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
genomic: AAAGTCC-TTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
EST: gi|60354010|gb|DN220983.1|DN220983
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
EST: gi|32840315|gb|CD979996.1|CD979996
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
EST: gi|18384842|gb|BM418041.1|BM418041
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGGAAAGGTTGCTGAGGCTCTGAAAGATAACAAA
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAA
EST: gi|67010636|gb|CO439385.1|CO439385
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
EST: gi|18384843|gb|BM418042.1|BM418042
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGGAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACA
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACA
EST: gi|16746087|gb|BM032517.1|BM032517
EST:     CAA-GTCCTT-CAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGGAAAGGTTGCTGAGGCTCTGAAAG
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAG
EST: gi|60346680|gb|DN213653.1|DN213653
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
EST: gi|12046108|gb|BF728247.1|BF728247
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGGAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACC
EST: gi|18384685|gb|BM417884.1|BM417884
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGGAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACA
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACA
EST: gi|18384683|gb|BM417882.1|BM417882
EST:     CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAG                         GGAGCTGGAAAGGTTGCTGAGGCTCTGAAAGAT
genomic: CAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGAT

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), 47 (downstream exon)
Score: 74

CAACATTAGCCCGGAAGGTTTACATCCTGTAGCCGAGTTCCTCAAAAGGACAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACCATAGACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

CAACATTAGCCCGGAAGGTTTACATCCTGTAGCCGAGTTCCTCAAAAGGACAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACCATAGACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

CAACATTAGCCCGGAAGGTTTACATCCTGTAGCCGAGTTCCTCAAAAGGACAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACCATAGACTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 72

CAACATTAGCCCGGAAGGTTTACATCCTGTAGCCGAGTTCCTCAAAAGGACAAAGTCCTTACAGTGGTTCAGTCTCTACATGAACGATATTAGTGATGAGgtaatactgt ... atttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACCATAGACTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttatgcatttcatttaatgaaccctgatgtatgttaaaatgaatttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACCATAGACTTG
                        ccctgat  putative branch site (score: 72)
                                              tttcacc  putative PPT
                                tatgttaaaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcacatgatttcccttgtatccagtgtgtacgcatgtttgtttatgcttatgcatttcatttaatgaaccctgatgtatgttaaaatgaatttcaccagGGAGCTGAAAAGGTTGCTGAGGCTCTGAAAGATAACAAAACAATTTCTACCATAGACTTG

- - catgatt
- - - - - - - - tgtatcc
- - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgatg