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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgctcgtacttcgtctaccttaatttctctgcacgtgcgctcgattcatgcctctggctctgagacggtattaaatttaaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC

Basic information

species Zea mays
transcript GRMZM2G000825_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000825_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 2
gttcgtgctcgtacttcgtctac-cttaatttctctgcacgtgcgctcgattcatgcctctggctctgagacggtattaaatttaaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC
||||   | |   ||||  || | |   ||| |||||||        | || |  ||  |  |||       |    | ||| | |    ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||| |||||||||||||||||||||||||||| ||||| ||||| |
gttcaatccccctcttccccttctcgccattgctctgcaa-------caatgcgcgcagcaagctgatgcgtgtcgatgaatctga----gcagAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC

upper sequence: GRMZM2G000825_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ30150 (Selaginella moellendorffii), 3'ss of exon 2
gttcgtgctcgtacttcgtctaccttaatttctctgcacgtgcgctcgattcatgcctctggctctgagacggtattaaatttaaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC
||  |  | | |  | |  | |    | | |||| | || ||   |||||  |   | ||| ||    | || |  |   | |     | ||||| || || ||||||||||| || ||| | || |||||||||||||| ||||||||| ||  ||||| ||||||||| |||||||||||||| || || |
gtaagccccctttttcccccaaatccagtctctcgg-acatgta-tcgatg-aaatcgctgactt--gggcgattctctctct-----cccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC

upper sequence: GRMZM2G000825_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ08332 (Selaginella moellendorffii), 3'ss of exon 2
gttcgtgctcgtacttcgtctaccttaatttctctgcacgtgcgctcgattcatgcctctggctctgagacggtattaaatttaaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC
||  |  | | |  | |  | |    | | |||| | || || | |||||  |   | ||| ||    | || |  |   | |     | ||||| || || ||||||||||| || ||| | || |||||||||||||| ||||||||| ||  ||||| ||||||||| |||||||||||||| || || |
gtaagccccctttttcccccaaatccagtctctcgg-acatg-gatcgatg-aaatcgctgactt--gggcgattctctctct-----cccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC

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|71427346|gb|DR808396.1|DR808396
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|50339882|gb|CO535008.1|CO535008
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|149206098|gb|ES701694.1|ES701694
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|78091042|gb|DV519416.1|DV519416
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|78074236|gb|DV502670.1|DV502670
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|71329748|gb|DR801587.1|DR801587
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|71332935|gb|DR803491.1|DR803491
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|94476522|gb|EB705480.1|EB705480
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|50338121|gb|CO533247.1|CO533247
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|91050311|gb|EB160729.1|EB160729
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|71427332|gb|DR808382.1|DR808382
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|78123617|gb|DV542001.1|DV542001
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|211431813|gb|FL298794.1|FL298794
EST:     CCGACCAGGCGCAGGARTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCG
EST: gi|91053161|gb|EB163579.1|EB163579
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|71773443|gb|DR971345.1|DR971345
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAAGCTGCA
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAA-GCTGCA
EST: gi|50324554|gb|CO519680.1|CO519680
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|91049686|gb|EB160104.1|EB160104
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|30031735|gb|CB833586.1|CB833586
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|50336187|gb|CO531313.1|CO531313
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|91872937|gb|EB402894.1|EB402894
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|211337530|gb|FK986455.1|FK986455
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCAC
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCAC
EST: gi|71773656|gb|DR971553.1|DR971553
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|71449759|gb|DR830809.1|DR830809
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|78091200|gb|DV519574.1|DV519574
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCCAATCTCGCTGCCTCAAGCACAAGCTGCA
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGC-TCAAGCACAAGCTGCA
EST: gi|71772102|gb|DR970039.1|DR970039
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|71771752|gb|DR969689.1|DR969689
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|78085350|gb|DV513743.1|DV513743
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCAC
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCAC
EST: gi|50339616|gb|CO534742.1|CO534742
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
EST: gi|71324131|gb|DR798765.1|DR798765
EST:     CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAG                         AGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAG

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: 98

CCGCGCCGAGGAGGCCATCGAGGCCATCAAGTCGCTGCGCAGCCGATGCTCCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC


Block sizes: 35 (upstream exon), 39 (downstream exon)
Score: 18

CCGCGCCGAGGAGGCCATCGAGGCCATCAAGTCGCTGCGCAGCCGATGCTCCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 18

CCGCGCCGAGGAGGCCATCGAGGCCATCAAGTCGCTGCGCAGCCGATGCTCCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC


Block sizes: 35 (upstream exon), 28 (downstream exon)
Score: 2

CCGCGCCGAGGAGGCCATCGAGGCCATCAAGTCGCTGCGCAGCCGATGCTCCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGATCTCTACAAGgttcgtgctc ... aaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgcgctcgattcatgcctctggctctgagacggtattaaatttaaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC
                                   tattaaatttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtgctcgtacttcgtctaccttaatttctctgcacgtgcgctcgattcatgcctctggctctgagacggtattaaatttaaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT