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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctattccgtacttttctttggctgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG

Basic information

species Zea mays
transcript GRMZM2G019267_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctattccgtacttttctttggctgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
                                                ||| |   ||        ||   |||       ||     | |  ||      ||   ||||     | | |||||     |     | || ||||||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| ||
----------------------------------------------gtatgctgcattaaccagttgtgacttttcagacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 9
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctattccgtacttttctttggc--tgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
                                            ||| |   ||| |  ||| |  |   | | ||||     ||     |  |||||         |||    | ||  |||| |   |  |    ||   ||||| ||  | || || |||||||||||||| || ||||||||||| ||||| |||||||| ||||| || ||
--------------------------------------------caataatattactcactactgggagatgtccttttatgatgaatcattctgttcttgatctgtattctaatatttgtttgccaaattgatttctcga-cagAGAATTACTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACGGATCCATTACCATGTGATCCTAAGAG

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 10
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctatt---ccgtacttttctttggctgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
                                             |||||  |||  | | | |   | | |   || | ||     |   | ||||| |       |||   | | ||  |||| |   | ||    |  | ||||| ||  | || ||||||||||||||||| || ||||||||||| ||||| ||||| |||||||| || ||
------------------------------------------aagaaaattattatctgccacttggctgcatggttttatgataatta-attttgtttatgatctgcatcctgatatttgtttgtcaattttat---ttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G44400.1 (Glycine max), 3'ss of exon 11
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctattccgtacttttctttggctgctgtgtgttgt-tcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
                                         |   ||||   ||| || | | |  |   | |  |||        |   || | |||       | | |   | ||  |||| |   |     | |  | ||||| ||  | || ||||||||||||||||| || ||||||||||| ||||| |||||||||||||| || ||
-----------------------------------------aaaaaaaaatattatttgccacttggctttatgattttatgataattaattttctcatgatctgcgtcttaatttttgtttgtcaattt---gatttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCATGCGATCCCAAGAG

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv00s0805g00020.t01 (Vitis vinifera), 3'ss of exon 8
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctattccgtacttttctttggc-tgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
                                  | | ||| | || | |  | | |   |  |   || |||| | ||   || ||| | || ||||    || |||||   | ||  ||| ||   | |          ||||| ||||| || || ||||| || ||||| ||||||||||||| ||| |||||||| |||||||| || ||
---------------------------------ctctctttcgacacagtt-tcattgatttgtttttaattttttctgatgtgttgtattttcttca---ttgacatttctttttttgtttaacttgtttgtg-------cagAGAATATCTGCCAAGGATGCTCTGGATGCTGAATATTTCTGGAATGACCCCTTACCTTGCGATCCCAAGAG

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 11
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctat-tccgtacttttctttggctgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
                                  ||||||||    |  || ||    | ||| | |  |||| | |||     || | | |   || |   | || | ||   ||| |||| |      ||||||  ||  |||| ||||| || || |||||||||||||| || |||||||||||||| || || || || ||||| || ||
----------------------------------tttgtttaaaggagttgattttagcatatatacacacttatattt-----ctctttctccctctctaatatcctatgtccctttttttaaaat---tacaaa--atgtagAGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAG

upper sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 9
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctattccgtacttttctttggctgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
              |||| |   ||    |||  |  |  | |  | | || ||    | |      | ||   |||   |  |   ||    |  | |||| | || || |  ||  ||  | |  | |        | ||| | || |  || ||||||||||| || || ||||||||||||||||| ||||| || ||| | ||||  ||
--------------gtgagt--gtgatcatttgttacgcattgggatattgcttcacactt-cagtatgctacgcttaaacatcctcgttacatcgaaacctcttatctgtgcattaattc-atggttttgt---ctgtgcagCGAATCTGTGCTAAAGATGCACTCGACGCCGAATATTTCTGGACTGAACCCTTTCCCTGCCAACCAAGCAG

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|93282558|gb|EB674822.1|EB674822
EST:     GACATGCACTGGATCTGTTAGAGAAGATGTTGACTTTAGATCCATCACAG                         AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCC
genomic: GACATGCACTGGATCTGTTAGAGAAGATGTTGACTTTAGATCCATCACAGgtatgctaca ... aatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCC
EST: gi|32804528|gb|CD956764.1|CD956764
EST:     GATCCATCACAG                         AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCC
genomic: GATCCATCACAGgtatgctaca ... aatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCC
EST: gi|32804625|gb|CD956861.1|CD956861
EST:     GATCCCTCACAG                         AGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCC
genomic: GATCCATCACAGgtatgctaca ... aatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG
                             ttttgac  putative branch site (score: 3)
                                            aaatcatt  TA-rich tract