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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

Basic information

species Zea mays
transcript GRMZM2G091265_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
----gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattat---ttttgcttctgatg-taat-----gtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
     ||  | || | |  |   || | | | | ||  |  ||     | |  |   | || | | |    |||| || |  || ||||     ||||   ||||| | ||  |||    ||| ||| |||| || || |||||||| ||||||||||| ||||||||||| || ||||||||||| || ||||||||||||||
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggt-ttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttt--tgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                       ||||  || | || |||  |  ||| | || |  | || |   || ||   |||    ||    ||||  |||| |  |  |   ||||     | ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| ||
-----------------------gtaagtttatttc-tgttttttttagtgagataatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgt---ggtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G34740.3 (Glycine max), 3'ss of exon 2
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttt--tgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG-------------------------------
       ||| | ||   |||||||    |||  | |  |  ||||      |||||| || |   || ||   |||    ||    ||||  |||| |  | ||   |||| | |   ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| ||                               
-----gtaagtttttttatttctgt---ttttactgagataatggtg---ttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttt---tgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGGTAAAACCAGTATATTCTGCTTTTTTTTGTT

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                       || |    ||||   |  | || |  |  |||| |   | |  ||   ||  | |  | |    || |||| ||| | |     | | ||| | ||||| |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| ||
--------------------gaggttattgattgtggggatggggattttgggttt-tggaactgatggggcttttctttttttcttttcttgaactttttttgtggtttgtgttt-tgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttt--tgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
       ||| | ||   |||||||    |||  | |  |  ||||      |||||| || |   || ||   |||    ||    ||||  |||| |  | ||   |||| | |   ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||||||||| || |||||||| ||
-----gtaagtttttttatttctgt---ttttactgagataatggtg---ttgtttgtgttttaagtgtttgaaatggtgggttttgttttgttgatttagtttggttttgtgttt---tgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
        ||   ||  |||  |      ||  | |  | || ||||        | | || |||||  ||  |  |    | |||      |  ||| | ||   |||| | |   ||||| |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| |||||||| ||
------ggaggggtttttttggt------ttcaggcccgagggggtt------ccttttttttttttttttggggggggggggggggcgggggggcttttttggt-ttgtgttt---tgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggtta-atcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtga--cattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                       ||||    | |  |  | ||  | | |||||         || ||  | |        |    ||||||| ||||  ||||     ||||| || | ||||| || ||||| ||||| ||||| ||||| || || || |||||||||||||||||||| ||||| |||||
-----------------------gtaag---tagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttatctgttgtgggttgttgttggt-tctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggt--ggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                       || |  ||  ||  | | |   | || ||  | ||| || |||     | ||| | |   ||||| |  |  ||  | |   |     ||||||| ||||| |||||||| || |||||||| || ||||| ||||| || ||||| ||||| || || |||||||||||
-----------------------gtgagtttgagttgttttgctggattgat--gattg-atgattgaatgtactggtatt-cgtgggctgatgaatacttttgaat----tttgtat-tgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0059g01180.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttg--cttctgat--gtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                                     |   | | |         || || | |  || | | |  |  |  ||| |  | ||| ||  |||  |   || ||||  | | ||   |||  ||||   | | ||     ||||  || | ||| ||||| ||||| |||||||| || || ||||| ||||| ||||||||||| |||||||||||||||||
gtgagtccgagttccattaaagattaaactgcatttagctcatagaagcagaaaattactttcaaattgt-taaactaataattacttggattggatgttttgagggtttttgattggcactgactgatgcttgaatgtttttgg----gttttgatttaaagGTATTGTAAGTGCGAGATGCCTTATAATCCGGACGACCTTATGGTGCAGTGCGAAGGATGCAAGGACTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------gtgtacaaagctcttccttttctgtaaccttttgtcat--gtggtggttaatcagtttgtatta--tttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                                                           ||||   ||       |   | |    | ||  ||| |  |||  |   | | |||  |  |||  ||| |||   | | |   |    |||||      | |  ||  || |  ||| |    || |||||||||||||||||||| |||||||| ||  || | ||| || | ||  |  | ||||| |||||
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgttt---cagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttg-tattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                                                 | || |||  |    | |  |||  |||    | |   ||  |   | || |  |     |||||       || || |||||||| |||||||| |||||||||||||| || |||||||||||||| |  ||||| |||||
------------------------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctctttttttgg-----gtttgcggaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ17782 (Selaginella moellendorffii), 3'ss of exon 2
------------------------------------------------------gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggattttt---gatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                                                         ||  |||||  || || |        | | ||  |||  |  |  | |   |  | || |  |||  |  ||  |  | |    | | |   | |||||     |  | ||  || |||||| |||||||||||||||||||| ||||| ||||| ||  | ||||| ||||| ||    |||||||| ||
gtaagtgctctctctctccctctgtctctctggcgtctcgttgactagttgtgttcttatcaagcttctctttcttctcttggtctcgttgtgttcttatcgaacttctcctgttctcgttgtgttcgaacttctctttcttctcttgtgttcttaccaagcgct-ttattacgtgaagGTATTGCAAGTGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

upper sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatg-tgacattgtttgtatgtgaa---gatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
                                                            ||   |||     | | | |  | ||||| |  |||||||| |  | || ||||  | ||||   | || |||||||| |||||||| |||||||||||||| || |||||||||||||| |  ||||| |||||
-----------------------------------------------------------gtaagattgacaaagctctcactttggattctctatcttatgctctctttttttgggtttgaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

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|7162430|gb|AW520052.1|AW520052
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCC                         TGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGC
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCgtgtacaaag ... atattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGC
EST: gi|148933222|gb|EC876874.2|EC876874
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCC                         G
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCgtgtacaaag ... atattgcaag-
EST: gi|148933222|gb|EC876874.2|EC876874
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCC                         G
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCgtgtacaaag ... atattgcaag-
EST: gi|94476085|gb|EB705043.1|EB705043
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCC                         G
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCgtgtacaaag ... atattgcaag-
EST: gi|94476085|gb|EB705043.1|EB705043
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCC                         G
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCgtgtacaaag ... atattgcaag-
EST: gi|78091413|gb|DV519787.1|DV519787
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCGTATATTGC                 
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCG-C--------Cgtgtacaaag ... at
EST: gi|78091413|gb|DV519787.1|DV519787
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCGTATATTGC                 
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCG-C--------Cgtgtacaaag ... at
EST: gi|78091413|gb|DV519787.1|DV519787
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCGTATATTGC                 
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCG-C--------Cgtgtacaaag ... at
EST: gi|78091413|gb|DV519787.1|DV519787
EST:     GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCGCCGTATATTGC                 
genomic: GATTTGACTACAAGGCCGCCACCGGTGCATTCACCCCCGACCGTGTCG-C--------Cgtgtacaaag ... at


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG
           ttttgat  putative branch site (score: 4)
         atttttgatcttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattatttttgcttctgatgtaatgtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG