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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccaccggtttggtcacatctgttctcggtggctgctggggccctaacaacagcaccaacctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG

Basic information

species Zea mays
transcript GRMZM2G478779_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 1
----------------------------gtgagccaccggtttggtcacatctgttctcggtggc-tgctgg-ggccctaacaacagcaccaacctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
                            ||| ||| |  | |    | | | |||||  |    | || ||  |||  |  |     | ||    || ||||||||| || ||||| || || |||||  | || || ||||||  ||||||||| || || |||||||| ||||| |||||||||||||| ||||||    
tccatttaacttgggcgttgggcctggcgtgggccccgcgctgcagcgcgt-tgttcgagcaaacctgatgctggcgatcgctgtgtcgccg-tgtccgcagGCTGGCTTTGCTGGTGATGATGCCCCTCGCGCTGTGTTCCCCTCCATCGTGGGCCGGCCCCGCCACACCGGTGTGATGGTCGGGATGGGCCAGAAG----

upper sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------gtgagccaccgg--tttggtcacatct-gttctcggtggctgctggggccctaacaacagcaccaacctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
                          |||    || |  |||| |  ||| |  || | |     | |  ||  ||  |    |    |||   | ||||||||| |||||  | ||||| |||||  |||| || |||||||||||||||||||| ||| | ||||| || || ||||| || ||||| ||||| ||||
gcatagcactgtgcattataaaggcatgaaatcccagcttttgatggcattttattgttgaataattccaggcgccggaattgaatttcaattgccgcagGCTGGTTTCGCCAGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
-------------------------gtgagccaccggtt-tggtcacatctgttctcggtggctgctggggccctaac-aacagcaccaacctcg--gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
                         |  || ||  || | | | |  || | |  ||  |  ||   |   |  |    ||        |  |    ||||||||| |||||||| ||||| || ||  | || || ||||||||||| || ||||||||  | |||||||| || |||||||| ||||| ||||||||||
ctcttttgcatctttatttataatgggcagacattggatgtagactaatttatgatcaatc-ctctcgaaactgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S198_154V6.3 (Physcomitrella patens), 3'ss of exon 2
-----------gtgagccaccggtttg----gtcacatctgttctcggtggctgctggggccc-taacaacagcaccaacctcg------------gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
           | |  ||  |  |||      |||| ||   | || |  | |       |   |||||  |  |  || | ||            ||||||||| |||||||| || ||||||||  | ||||| || || ||||||||||| || ||| | ||||||||||| |||||||| ||||| ||||||||||
aaccttaacttgcgtaccctcaatttttatcatcacttcatctgtctggagttcacatctcttgtaacatgatgagtaatcacgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S198_157V6.3 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------------------gtgagccaccggtttggtcacatc-tgtt--ctcggtggctgctg-gggccctaaca-------acagcaccaacctcg-gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
                                                                                                    |   |  | ||  ||  ||||||| || |  ||| |||   |        ||||| |       |  |  |  |  |   ||||||||| |||||||| || ||||||||  | ||||| || || ||||||||||| || ||| | ||||||||||| |||||||| ||||| ||||||||||
gtatgatattaactgttttgatgatgcatttgtattctccctatgtgatgaagtggcttgcaataaaatgcagttctaaagcatgtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------gtga-gccaccggtttggtcacatctgttct-cggtggctgctggggccctaac-aacagcaccaacctcg--gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
                        |||    ||   |   || || || ||| | | ||       |   || |    ||  |     |  |    ||||||||| |||||||| ||||| || ||  | || || ||||||||||| || ||||||||  | |||||||| || |||||||| ||||| ||||||||||
caattcatgctataatggcgttcatgataatactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------------gtgagccaccgg--tttggtcacatctgttctcggtg-gctgctggggccctaacaacagcaccaacctcg-----gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
                                                                                               | |  ||  |   | |   || ||| || ||| |     |||       || | |  ||  |     |       ||||||||| ||||| || ||||| |||||  |||| || |||||||||||||||||||| ||| | ||||| || || ||||| || ||||| ||||| ||||
gtatgcatgcttaccgcatatacgactgtaattctcccatgcaaatcgagcatgctaacaatcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcgcagGCTGGTTTCGCCGGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: GRMZM2G478779_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------gtgagccaccggtttggtcacatc-tgtt--ctcggtggctgctg-gggccctaaca-------acagcaccaacctcg-gcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
                |   |  | ||  ||  ||||||| || |  ||| |||   |        ||||| |       |  |  |  |  |   ||||||||| |||||||| || ||||||||  | ||||| || || ||||||||||| || ||| | ||||||||||| |||||||| ||||| ||||||||||
gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

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|14701188|gb|BI233606.1|BI233606
EST:     CCG-GGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTG
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtgagccacc ... acctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTG
EST: gi|18965167|gb|BM661429.1|BM661429
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTG
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtgagccacc ... acctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTG
EST: gi|19058066|gb|BM736733.1|BM736733
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCTGGCGTCGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTG
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtgagccacc ... acctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTG
EST: gi|21390301|gb|BQ528350.1|BQ528350
EST:     ACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCTCAGCATCGT
genomic: ACGGAACTGGCATGGTCAAGgtgagccacc ... acctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCC-CAGCATCGT
EST: gi|8103062|gb|AW927727.1|AW927727
EST:     CCGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAG                         GCTGGGTTCGCCGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTG
genomic: CCGAGGATATCCAGCCCCTCGTCTGCGACAACGGAACTGGCATGGTCAAGgtgagccacc ... acctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacatctgttctcggtggctgctggggccctaacaacagcaccaacctcggcagGCTGGGTTCGCTGGCGACGACGCCCCGAGGGCCGTCTTCCCCAGCATCGTGGGGCGCCCGCGCCACACTGGTGTCATGGTCGGGATGGGGCAGAAGGACG
                            ccctaac  putative branch site (score: 2)