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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaatagattggcctcttatttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG

Basic information

species Zea mays
transcript GRMZM2G011518_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 1
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaatagattggcctcttatttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
     ||  |     ||||    || |    |  | |   |||  |  |||||   | || ||||  |   || |         |  ||||      |||||||||||||||||| | ||||| || ||||| |||||||||||||||||||| ||||| || |||||||||||||| ||||| || ||||
----gtaccccaagcttttccactcttgtctgtctcgtctcagattgggttttggacggatcatggat--gatgg---------tggttttggctggcagGTGGTGATGCTTGGGCTAGATGCCGCGGGGAAGACCACCATACTCTATAAGCTGCACATCGGCGAAGTTCTCTCCACCGTCCCCACTATAG

upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 2
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaa-tagattggcctctt-atttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
       ||    || |  |   |  |   |  |||             |||||  || ||  |     ||| |  |||     ||| || | |||  |||||| |||||||||||  | ||||| ||||| ||||| || ||||| || ||| |||||||||| |||||| | ||||| || ||||| || |
-------gtaactttctgcttgcttgttaaacgttaa----------ttttttacactcaatttattattaactttattatttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGTTTCACATTGGAGAAGTTTTATCCACCGTTCCTACAATTG

upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 1
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgt--tttaagctgaacatgcctctaatagattggcctcttatttttttcc---tcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
     | || ||  ||  |   ||||||     |   | |    |||| |  | |  ||   |  | ||     ||  ||    | |||  ||| |     | |||| |||||||||||  | ||||| ||||| ||||| || ||||| || ||||| |||||||| |||||| | || ||||| ||||| ||||
-----ttgtttttcttagtctcatcatccatcttctaaccatagatccttgatctttgcatgagtttccgtacttactttttttttttacatttgttgggattagGTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG

upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 2
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaatagattggcctctt-atttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
       ||    || |  |  ||  |   |  |||             |||||  || ||      |  | |  |||     ||| || | |||  |||||| |||||||||||  | ||||| ||||| ||||| || ||||| || |||||||||||||| |||||| | |||||||| ||||| || |
-------gtaactttctgcttgattgttaaatgttaat-----------ttttacactcaattattattaattttattatttccttgatctgtttgttcagGTTGTGATGCTTGGTCTTGATGCTGCTGGCAAAACAACTATACTTTACAAGCTTCACATTGGAGAAGTTTTATCCACTGTTCCTACAATTG

upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G09790.2 (Glycine max), 3'ss of exon 1
---------atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaatagattggcctcttatttttttc-ctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
         ||  || || ||  || ||   ||||||  |  ||  || || |     | || | ||   || |  | |        |  ||   |||| ||    | |||| |||||||||||  | ||||| ||||| ||||| || ||||| || ||||| |||||||| |||||| | || ||||| ||||| ||||
tgttcgttaatactt-gtgtttcttattctcatcatcc-atcttctaatcattgat--tcttgatctatgcacgagttt------ccgtacttacatttgttgggtttagGTTGTGATGCTTGGTCTAGATGCTGCTGGCAAAACAACTATACTGTACAAGCTCCACATTGGAGAAGTTTTATCTACTGTTCCTACAATAG

upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 1
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaatagattggcctcttatttttttcc-tcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
 | ||      | | |   | |||  |      |||       | ||  | |     |  |  |   | |  ||  |       | |||   ||   | |||| |||||||||||  ||||||||||||| ||||| |||||||| || ||  | |||||||| |||||| | |||||||| || || || |
-tattcttgagtttatgcctgtattcttaatatttattcatgatttctctatgtccttcgagcttattttcttatttaaattattaattgagttggattagGTTGTGATGCTTGGCCTGGATGCAGCTGGTAAAACAACCATACTGTACAAATTGCACATTGGAGAAGTTTTGTCCACTGTTCCCACAATTG

upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 3'ss of exon 1
atgtttagtcttcttttttta-tatcat-cggagattagaaccagtatccgttttaagctgaacatgcctctaatagattggcctcttatttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
   | ||||   | ||||  | || ||| |  || ||        |     |    |  |  ||  |     ||  | || |  ||| || | | |   ||||||||||||||||| ||||| || || || ||||| ||||| |||||||||||||| || || ||  |||| ||||| || |||||||| |
-cttctagttgaccttttgaagtaacattcaaagcttcaggatgttgatgatagagatttacacggggaataaaatggttcgtgtctcatgtatctgg-cagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACTACCATTCTCTATAAGCTTCATATCGGGGAGATTCTATCCACCGTTCCTACCATTG

upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 1
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctc-taatagattg-gcctcttatttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
   || |    | |     |   |  |  |||| | |    | | |   | |  |  |  |   |  |  | ||    || || ||| || | | |  | |||||||||||||||| ||||| || || || ||||||||||| ||||||||||| || ||||| ||  || | ||||| ||||| ||||| |
-ctttcatcactttcagcctggctactgagagaattgctttattttaactatagaaattcatgcgggtaatgatgtgctgtgcatctcatgtatctgat-agGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG

upper sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 1
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctctaatagattgg--cctcttatttttttcct------cagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
        || |||   |||  |||   |    |||||   || || |  |  | |  | |||| ||| | ||  |  |     |||||   || |  |      ||||| ||||||||||| || |||||||| || ||||||||||| |||||||||||||||||||| ||  |||| ||||| || || ||||| |
------gttcatctacatttgaatcgatgttttttaga--tagaattccatacaggaagcacattcctgtgatttaccgagatttcttacgattcttgtatctgccagGTTGTGATGCTTGGTTTAGATGCAGCAGGCAAAACCACCATCCTCTATAAGCTTCACATTGGAGAGATTCTGTCCACCGTTCCCACCATTG

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|211532195|gb|FL238607.1|FL238607
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
EST: gi|74243860|gb|DT651774.1|DT651774
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
EST: gi|211532186|gb|FL238598.1|FL238598
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
EST: gi|211535184|gb|FL238611.1|FL238611
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
EST: gi|211532185|gb|FL238597.1|FL238597
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
EST: gi|211535181|gb|FL238608.1|FL238608
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
EST: gi|211532189|gb|FL238601.1|FL238601
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
EST: gi|211532184|gb|FL238596.1|FL238596
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
EST: gi|76932677|gb|DV173113.1|DV173113
EST:     AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG
genomic: AGGCCTTCCGAAAGCTGTTTGATGCCTTCTTCGGCAACAAGGAGATGCGGgtacgctgtc ... ttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgttttaagctgaacatgcctctaatagattggcctcttatttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
                     ctctaat  putative branch site (score: 3)
                               ttggcctcttattttt  putative PPT
                                     tcttattttttt  TA-rich tract