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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattacctactatcagcatcatcacacaaacacaagacagaacatgtcaatgtcactcatcactcactctcctgtccag

Basic information

species Zea mays
transcript GRMZM2G063949_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 2
ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattacctactatcagcatca----tcacacaaacacaagacagaacatgt-caatgtcactcatcactcactctcctgtccag--
|| || |||||||| ||||||||||||||||||||||||||||| ||||| || ||||||||||||||||||||||||||||| ||||| ||||||      |||  | ||  |  ||    ||               |  ||  || ||   |   | ||       | |  ||| ||   
ACGATCAACCTGGCGGCGATCTGCACGCCGGCCGACTACAACACGCGCCCCCTCGACACCATCTACAGCAACTTCATCGACGCGCTCCCTGTGgtaatccctcctcttctccactccagatttcttcttcttcttttctaccactagtgcagaattgttgatggacgtgtgtgatgtgcacag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 2
ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattacctactatcagcatcatcacacaaacacaagacagaacatgtcaatgtcactcatcactcactctcctgtccag----------
|| || || ||||| ||||| ||||| || || || |||||||||||||| || |||||||| |||||||| ||||||||||| ||||| ||||||   | ||  || | | |  |||      |||    | ||     || |  | |       |      |      ||   |          
ACTATTAATCTGGCTGCGATTTGCACTCCCGCGGATTACAACACTCGCCCTCTCGACACCATTTACAGCAATTTCATCGACGCGCTCCCCGTGgta-actaactaaccacctgt-tcaaattgaaaatgtgaaacgctgaatcttgagggtttgagttctatgcgacgtcgttttgtgctttgtag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 2
ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattacctact--atcagcatcatcacacaaacacaagacagaacatgtcaatgtcactcatcactcactctcctgtccag----------------------
|| || || ||||| || || ||||| || || || |||||||| ||||| || |||||||| |||||||| ||||||||||| ||||| ||||||   ||| |||||  |  | |  |       ||   |||    |||  |||  |  ||    || | |     ||   || |                       
ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACCCGCCCTCTCGACACCATTTACAGCAATTTCATCGACGCGCTCCCCGTGgta-acttaactacttcactaactacccgttctaattgcaaatgtgaat-tgttga-atcttgaatgatttgagttcgattcgacgtcgtttcgttcttttttgtag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA12G30490.2 (Glycine max), 5'ss of exon 2
ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattacctacta-tcagcatcatcacacaaacacaaga-----cagaacatgtcaatgtc---actcatcactcactctcctgtccag
|| || || ||||| || || ||||| || || || |||||||| ||||| |||||||| || |||||||||||||||||||| || || ||||| ||  |  ||  || |   | |  || | |               | |    | |  |  |    | | |  | |     |   || |||
ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTGgtgcgtcttacttttactttactttctctcccttttttctttgttttctgtgtgtttggaaattcaaattgaggattggaatttgggttcag

upper sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 2
ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacg-attacctactatcagcatcatcacacaaacacaagacagaacatgtcaatgtcactcatcactcactctcctgtccag-----------------------------------------
|| ||||| || || |||||||| || || || || ||||| || || || |||||||| ||||||||||| ||||| || || |||||||||||| | |||   | || |  |||   |         |   ||   |   ||| | | | |   ||   |   | |  |    |                                          
ACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTGgtatgtattttatgct-tttgcagtttgtttggtttagtggagcaattttgtaagtttgaggaatatttttatgtgatacggattttagttgtgacattgagtggtcattggttttggtatgtag

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|149113013|gb|EE295788.2|EE295788
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|149080206|gb|EE169228.2|EE169228
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|211213921|gb|FL245928.1|FL245928
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|67020065|gb|CO448814.1|CO448814
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|109637685|gb|EC591230.1|EC591230
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|149086197|gb|EE175737.2|EE175737
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|101398997|gb|EB821371.1|EB821371
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|40337281|gb|CK371351.1|CK371351
EST:     CAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|211216493|gb|FL245943.1|FL245943
EST:     CTCGCCCACTCGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|116817633|gb|EC860508.1|EC860508
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|211216498|gb|FL245948.1|FL245948
EST:     CTCGCCCACTCGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCT
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCT
EST: gi|211213924|gb|FL245931.1|FL245931
EST:     CTCGCCCACTCGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|22472630|gb|BU037110.1|BU037110
EST:     CTCGCCCACTCGACACCATCTACAGCAACTTCATCGACGCACTCCCAGGG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|67020590|gb|CO449339.1|CO449339
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|67011006|gb|CO439755.1|CO439755
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|211216491|gb|FL245941.1|FL245941
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|211216495|gb|FL245945.1|FL245945
EST:     CTCGCCCACTCGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGC
EST: gi|31356398|gb|CD440755.1|CD440755
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|211213923|gb|FL245930.1|FL245930
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|93281901|gb|EB674165.1|EB674165
EST:     TCGCCCACTTGACACCCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTG
genomic: TCGCCCACTTGACACC-ATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTG
EST: gi|31355714|gb|CD440071.1|CD440071
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|61118012|gb|DN558973.1|DN558973
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|149098034|gb|EE183981.2|EE183981
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|211216496|gb|FL245946.1|FL245946
EST:     CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGC
EST: gi|211213922|gb|FL245929.1|FL245929
EST:     CTCGCCCACTCGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG                         GTCAAGTACTGCTCCGAGAA
genomic: CTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAA

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: 299

ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGCGAGGTCTACGGCAAGACCATCGGCAGCTTCCTCCCCAAAGACCACCCGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 119

ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGCGAGGTCTACGGCAAGACCATCGGCAGCTTCCTCCCCAAAGACCACCCGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 63

ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGCGAGGTCTACGGCAAGACCATCGGCAGCTTCCTCCCCAAAGACCACCCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

ACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTGgtacgattac ... tcctgtccagGTCAAGTACTGCTCCGAGAACAGCAAGCGTCTCATCCACTTCTCCACCTGCGAGGTCTACGGCAAGACCATCGGCAGCTTCCTCCCCAAAGACCACCCGC