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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttcgcgctttccttaaccagagcctgtgtgagcgaggtttactgacccgcggaagacattgctgcctgtctgtgtgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATACGGCATGACGAGAGCGGCACGCGGACCGTGTGCGGCCGGCCGGAGT

Basic information

species Zea mays
transcript GRMZM2G024315_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024315_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g43090.1 (Oryza sativa), 3'ss of exon 2
gttcgttcgcg--ctttccttaaccagagcctgtgtga----gcgaggtttactgacccgcggaagacattgctgcctgtctgtgtgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATACGGCATGACGAGAGCGGCACGCGGACCGTGTGCGGCCGGCCGGAGT
||  | ||| |  | |||| |  |   | | |  |||       | ||||   |     |  || ||  |  |  | |  |  |  |  || |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||  | ||    ||||  |||  |||||||||||||||||||||
gtctggtcggggcccttcccttccttcatcgttcgtggtttcttgtggttggattggatgatgatgagctaaccccatcgccttcggatttccagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATTCGGCGGGGCGCCGACGGCGTGCGCGCCGTGTGCGGCCGGCCGGAGT
















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|71773863|gb|DR971754.1|DR971754
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|211083193|gb|FL315299.1|FL315299
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|76014741|gb|DT941911.1|DT941911
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|8367347|gb|BE050292.1|BE050292
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|148966879|gb|EE017999.2|EE017999
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|149109975|gb|EE293785.2|EE293785
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|211115050|gb|FL357310.1|FL357310
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|18450430|gb|BM428708.1|BM428708
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|18649258|gb|BM498077.1|BM498077
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|71438898|gb|DR819948.1|DR819948
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|211043426|gb|FL323571.1|FL323571
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|71430218|gb|DR811268.1|DR811268
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|19822526|gb|BQ048550.1|BQ048550
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|211435265|gb|FL220469.1|FL220469
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|71438372|gb|DR819422.1|DR819422
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|211312220|gb|FL336750.1|FL336750
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|211482867|gb|FL313329.1|FL313329
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|71327903|gb|DR800586.1|DR800586
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|149014830|gb|EE044532.2|EE044532
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|148931634|gb|EC874774.2|EC874774
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|211525034|gb|FL310989.1|FL310989
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
EST: gi|78090111|gb|DV518485.1|DV518485
EST:     ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAG                         GCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG
genomic: ACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGG

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: 47 (upstream exon), 49 (downstream exon)
Score: 98

CGGCATCGCCGTCATCGCGCACGCTTTCAGCCGCGGAGTCACCTTGTTCGACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATACGGCATGACGAGAGCGGCACGCGGACCGTGTGCGGCCGGCCGGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 560

CGGCATCGCCGTCATCGCGCACGCTTTCAGCCGCGGAGTCACCTTGTTCGACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATACGGCATGACGAGAGCGGCACGCGGACCGTGTGCGGCCGGCCGGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 704

CGGCATCGCCGTCATCGCGCACGCTTTCAGCCGCGGAGTCACCTTGTTCGACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATACGGCATGACGAGAGCGGCACGCGGACCGTGTGCGGCCGGCCGGAGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 130

CGGCATCGCCGTCATCGCGCACGCTTTCAGCCGCGGAGTCACCTTGTTCGACACCTCCGACGTATACGGGCCCCTCACCAACGAAATCCTCCTCGGCAAGgttcgttcgc ... tgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATACGGCATGACGAGAGCGGCACGCGGACCGTGTGCGGCCGGCCGGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcgaggtttactgacccgcggaagacattgctgcctgtctgtgtgcgttgcagGCGCTGAAGCAGCTGCCGCGGGAGCAGGTGCAGGTGGCCACCAAGTTCGGGATACGGCATGACGAGAGCGGCACGCGGACCGTGTGCGGCCGGCCGGAGT
          tactgac  putative branch site (score: 130)