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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttattttttgtaattaaagaagtggaattaatgtcatttgaggtttggctcaagactgtaaggtggataagtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC

Basic information

species Zea mays
transcript GRMZM2G104418_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 10
-cttattttttgtaattaaagaagtggaattaatgtcatttgaggtttggctcaagactgtaaggtggataagtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
  |||   ||      | || ||     |   |  |   |    ||||||  ||| |  ||   ||    || || | |   ||| || ||| || |||||  |||||||||||||||||||||| ||||| |||||||| || || ||||| |||||  ||||||| ||||||||||| |||||||| ||||| ||||||
aattagcattgactcctgaaaaatcaataaagagcttgctgtttgtttgggccaa-atggtttagttaggaactgctaactttgtattacatctgatacagGATAGCCAAATATCAAGAAGCAAACCCTGGTGTATTCACTATTGTCACTTTTCCTTTCTTATTTGCTGTCATGTTTGGAGATTGGGGACATGGAATTTGC

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
cttattttttgtaattaaagaagtggaattaatgtcatttgaggtttggctcaagactgtaaggtggataa-gtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
   |  |||  |  |||    | |     |  ||  || |    ||  | |   |   ||    || ||    ||    | || || ||  |    | |||||| ||||||||||| || || |||||| | |||||||| || || || ||||| || || ||||| || ||||||||||| ||||| ||||| || |||
-caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtctcttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
----------------cttattttttgtaattaaagaagtgg--aattaatgtcatttgaggtttggctcaagactgtaaggtgga-taagtgttgatgctgt----gttccatgtgg---------tacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
                    |||   | | || |||||  ||  |||| | |  |      |  |      | | |||   || || |  || ||  |  |||    ||| | | ||          | |||||| ||||| ||||| ||||| ||||| || ||||||||||| || || ||||| || || || || || ||||||||||||||||| ||||| || |||
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttgtagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 10
cttattttttgtaattaaagaagtggaattaatgtcatttgaggt-ttggctcaagactgtaaggtggataagtgttgatgctgtgt---tccatgtggt-acagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
    | ||||    | |   |  ||   || || |   |   | | |    | || |   |    ||  | | |  | |   | |||   ||||| |  |  ||| || ||||| |||||||| ||||||||||| |||||||| || || || || || ||||| ||||| |||||||||||||||||||| |||||  | |||
----tattttactttaacctatttgattttcattttgctgatgatatcaaattaacagaattgtttgcctca-tactaaaattatgtgattccatttaattgcagGGTGGCCAAGTATCAAGAGGCAAATCCTGGTGTATTCACTATTGTTACATTTCCATTTCTTTTTGCTGTCATGTTTGGTGATTGGGGACATGGATTATGC

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 10
cttatt-ttttgtaattaaagaagtggaattaatgtcatttgaggtttggctcaagactgtaaggtggataagtgttgatgctgtgttccat--gtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
 || || ||||  || |      |    ||  | || | |||       | | |||   | |   |  |  |||   |||    |  | ||    |  | ||| || ||||| ||||| ||||  |||||||| |||| |   ||  | || |||||||| || ||||| || ||||||||||||||||||||||| || |||
-ttgttatttttcaaatggtattgccctatagaagt-acttggctaaatgtttaag-tggcatcatccaatagtagagatcaactaattcaataatatttcagGGTGGCCAAGTATCAGGAAGTGAATCCTGGTGTATACGTGATTATTACATTCCCTTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGC

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S107_75V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------cttattttttg-taattaaagaagtggaattaatgtcatttgaggtt-tggctcaagactgtaaggtggataagtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
                                      ||   || ||| | ||    |   |  | |         ||| |||  ||| |     |  |    |   | |||  ||||    ||||     |  | |||||| |     ||||| |||||||||||||||   || |||||  | ||||||||||| ||||| || || ||||||||||| ||||| ||||| || || 
gtaagtgtgcagatcaacgatattacgacgcgttgaaactgggttgttgatgatcgctgttttcaactgctaagggattgtggtaatggttgttttcctttctttcattcagttctgatcagatgttgtgaata-tgcagTGTGGGACGGTATCAGGAAGCAAATCCTGGATGTTTTACCATAATAACTTTCCCTTTCCTATTCGCTGTTATGTTTGGTGACTGGGGACATGGAATCTGT

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ10256 (Selaginella moellendorffii), 3'ss of exon 9
cttattttttgtaattaaagaagtggaattaatgtcatttgaggtttggctcaagactgtaaggtggataagtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
                                           ||  |  |    ||  | |  ||| | ||| || |||    ||    ||   | |||||| |  | ||||||||||||||| || ||||| |||||||||||||| || || |||||||| || ||||||||||| || ||||| || || |||  |
-------------------------------------------gtaagcttgtgaaccattat-tggctgagtctt-atg----gtcttttggtctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGAGACTGGGGTCACGGAATTGTC

upper sequence: GRMZM2G104418_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
cttattttttgtaattaaagaagtggaattaatgtcatttgaggtttggctcaagactgtaaggtggataagtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
                                       | || ||  |   |  | | |  | ||   ||    | |||    ||    ||   | |||||| |  | ||||||||||||||| || ||||| |||||||||||||| || || |||||||| || ||||||||||| || ||||| || || |||  |
--------------------------------------gtaagatt--gtgaaccattattggctgacaaaagtcttatg----gtcttttggcctccagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC

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|32929086|gb|CF033898.1|CF033898
EST:     CAGCGTTCCAGGAAATTGTTGATGCATATGG                         TGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTT
genomic: CAGCGTTCCAGGAAATTGTTGATGCATATGGgtatgttttc ... tgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTT
EST: gi|32929323|gb|CF034135.1|CF034135
EST:     CAGCGTTCCAGGAAATTGTTGATGCATATGG                         TGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTT
genomic: CAGCGTTCCAGGAAATTGTTGATGCATATGGgtatgttttc ... tgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTT
EST: gi|32928488|gb|CF033300.1|CF033300
EST:     CTTCAGCGTTCCAGGAAATTGTTGATGCATATGG                         TGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTT
genomic: CTTCAGCGTTCCAGGAAATTGTTGATGCATATGGgtatgttttc ... tgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggctcaagactgtaaggtggataagtgttgatgctgtgttccatgtggtacagTGTAGCCAAATATCAAGAAGCAAATCCTGGAGTATTCACCATCGTGACTTTCCCTTTTCTATTTGCCGTCATGTTTGGTGATTGGGGCCATGGGATTTGC
                           tgttgat  putative branch site (score: 4)