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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaagaatcacatatagtgatggggtggcgtatttgattgtttagaccggataccgtgcagtttggatttatctcttttctgttttgtttcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

Basic information

species Zea mays
transcript GRMZM2G152757_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152757_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 1
--------aaaaagaatcacatatagtgatggggtggcgtatttgattgtttagaccggataccg-tgcagtttggatttatctcttttctgttttgtttcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
         ||||| |   |    | | |||     |   |||  |      |||    || | | |  | |   |||| || |||| | ||| | ||||      |||| ||| ||  ||| | || |||| || |  || ||  | ||| |||||||||||||||||||||||||||||||||
ttctttttcaaaagtactgcgacgattaatgc--ctgaaaattaaacga---agaggaaatgctggtataatactgattgat-tcttctttgtatggtttgt---acagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

upper sequence: GRMZM2G152757_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G26250.2 (Glycine max), 3'ss of exon 1
aaaaagaatcacatatagtgatggggtggcgtatttgattgtttagaccggataccgtgcagtttggatttatctcttttctgttttgtttcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
      ||   | |  |  |||      || |     ||||  |  |    | |  |   | |  | | | ||   || |  ||| |||    |   |||| ||||||  ||| | || |||| || |  || ||  | ||| |||||||||||||||||||||||||||||||||
-----taagtgc-tgcaacgatcaa--tgcctgaagaattgaatgaagaaaaaaatgctta-tgggtactgattgattcttcgttgtgtggtttgtgcagaaagttcagAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

upper sequence: GRMZM2G152757_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G26250.1 (Glycine max), 3'ss of exon 1
aaaaagaatcacatatagtgatggggtggc--gtatttgattgtttagacc--ggataccgtgcagtttgg-atttatctcttttctgttttgtttcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
        |       |||| ||    |     |   |||    ||  |    | | |   |||   | || | | ||   || |  ||| |||    |   |||| ||||||  ||| | || |||| || |  || ||  | ||| |||||||||||||||||||||||||||||||||
-----ctttttttctaagtgctgcaacgatcaatgcctgaagaattgaatgaagaaaaaaatgcttatgggtactgattgattcttcgttgtgtggtttgtgcagAAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

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|15208795|gb|BI430679.1|BI430679
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211084814|gb|FL392700.1|FL392700
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|91048113|gb|EB158531.1|EB158531
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211027069|gb|FL381517.1|FL381517
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211140497|gb|FL400397.1|FL400397
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|91052007|gb|EB162425.1|EB162425
EST:     GCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCCGCCAA-CTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: GCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCC-GCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211426998|gb|FL426768.1|FL426768
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|71435796|gb|DR816846.1|DR816846
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|67013898|gb|CO442647.1|CO442647
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211225357|gb|FL370946.1|FL370946
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|50326445|gb|CO521571.1|CO521571
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|149037768|gb|EE155430.2|EE155430
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|93012264|gb|EB637784.1|EB637784
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211337258|gb|FK972906.1|FK972906
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211131362|gb|FL428332.1|FL428332
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211217102|gb|FL383485.1|FL383485
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211335104|gb|FK972901.1|FK972901
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
EST: gi|211337263|gb|FK972911.1|FK972911
EST:     AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAG                         ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA
genomic: AGCTCGCCGCCGCCAAGAAGGCCGTCACCCTCGCCGCCAAACTCTGCCAGgttcgtggct ... tcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccggataccgtgcagtttggatttatctcttttctgttttgtttcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
                       tttatctcttttctgt  CT-rich tract
                      atttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaagaatcacatatagtgatggggtggcgtatttgattgtttagaccggataccgtgcagtttggatttatctcttttctgttttgtttcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT