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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA

Basic information

species Zea mays
transcript GRMZM2G064695_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggt-tatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
                                                                     | |    ||||||| | | | |       || |    ||   |||    |  |  | |      |   | | | ||| |  | | | | |      |||||| ||||||| |||||||||||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||| || ||||||||||| ||||| || ||||| || |
-------------------------------------------------------------------gaggatggcttgacttgcctctggagggatgttac----agcttttgttgttctgagaatggaaactgaagatatttatgagtttatctcta------atacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
                                                         | || ||||| |||     |||| |    || || |||||| | |     |||| | | |           ||||||  || || | |||  |              ||   || ||||||  ||||||| || |||||||| || ||||||||  | |||||||| ||||| |||||||||||||||||||| || || ||||| || |||||||| |
-------------------------------------------------------catgatctgtttgtgc-----ttgatta---ttaagcccttatatcctt---gaaccttcttt----------ctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 8
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
                                                         | || ||||| |||     |||| |    || || |||||| | |     |||  | | | ||   |  ||||   | |  || | || || |  ||     |||       || ||||||  ||||||| || ||||| || || ||||||||  | |||||||| || || |||||||||||||||||||| || || ||||| || |||||||| |
---------------------------------------------------------ttatctgtttgtgc-----ttgatta---ttaagcccttatatcctt---gaatcttcttttt---ttttactgggtgtgtgtaacattatgtgtgccttttaact-----ttgaacagGTGACTGCTGCAAAGGCAGACTTAAATTATATTGGGTTAGATGGAGAAATAGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 8
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaac-caatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
                                                                                  ||  | ||   ||| | | |    ||||   |||       |  ||  ||  || | |   ||  |   || |  ||       |  ||  | |||| |||||||| ||||  ||  ||||||| || ||| | ||||||||||||||||||||||||||||| || |||||||||||||| |||||||| || |
-------------------------------------------------------------------------------gtctctgtctatctcttgtat-catcaagaaa--gcc-----attgttatgttaattcgataggatgttaaaaggaatagtgtgttgtgtct-catagGTGGCTGCTGCTAAAGTTGACCTGAACTACATCGGTTTAGATGGAGAGATTGGTTGCATGGTGAATGGTGCTGGATTGGCCATGGCAACCATGGACATCA

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 8
gtataaaattacctatctttccatttgttcattctctcct-tgtgtcaagttttcttctaat-gtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
   |    |||| |  ||||  |||| || |  || |  | | ||| | ||        | | |    | | || |   | |   |  |     |  | ||  | |  | ||  |    || |   |  |    | | |  |  | || |    |   ||    |  |||    | |||| |||||||||||||||||||||||||| || ||  | |||||||| |||||||||||||||||||| || || || || ||||| ||||||||||| |
--gttgggttactt--cttttaatttcttgaccctgttttatctgtgatgtaagtggaaagtagcacatgtacataccataaaggcaatccc-cctctcttcacaactacaaggtaaaactaaagaacaa----tatgtaatgttctatttgtggtttca----ctgtaca---atagGTGGCTGCTGCCAAAGCAGATTTGAACTACATCGGCTTAGATGGAGAAATTGGTTGCATGGTGAATGGTGCTGGCTTAGCAATGGCTACCATGGATATAA

upper sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ13492 (Selaginella moellendorffii), 3'ss of exon 8
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
                                                                                                                      || |  ||  ||| ||  | |||  |   | | |   || |  | || |     |||||||||||||||    || ||||||||||| |||||  | ||||| |||||||| ||||||||||||||||||||| | || ||||| ||||||||||| |
---------------------------------------------------------------------------------------------------------------------gtttg--agaccttgttcatagtttcacg-ttttaatgcctgttcgaaaa-----acagGTCGCTGCTGCTGCCGCCGATTTGAACTACATTGGATTGGATGGCGAGATTGGCTGCATGGTGAATGGAGCAGGACTCGCGATGGCAACCATGGATATCA

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|18162086|gb|BM331925.1|BM331925
EST:     AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAG                         GTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
genomic: AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAGgtataaaatt ... acctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
EST: gi|60398611|gb|DN231427.1|DN231427
EST:     AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAG                         GTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
genomic: AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAGgtataaaatt ... acctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
EST: gi|211240437|gb|FL261944.1|FL261944
EST:     AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAG                         GTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
genomic: AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAGgtataaaatt ... acctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
EST: gi|211240439|gb|FL261946.1|FL261946
EST:     AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAG                         GTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
genomic: AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAGgtataaaatt ... acctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
EST: gi|60354613|gb|DN221586.1|DN221586
EST:     AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAG                         GTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT
genomic: AGAAAGAAATATTTGCACTGCGTGATACAACTCAGGAAGACCCCAGGGAGgtataaaatt ... acctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA
     tacttttttttggtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA