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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttggatcttctataaattaattatgtggatgactatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG

Basic information

species Zea mays
transcript GRMZM2G025854_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
gtatgctttggatcttctataaattaattatgtggatgactatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG
||||| |||  | ||| | | | || ||| ||||  | ||||||   |||         |||| || ||   |   ||||  |  | | |||||||||||| ||||| ||||||||||||||||||||||||||||| ||||| ||||| |||||||| |||
gtatgttttacaccttttttca-ttcattgtgtgcttcactatcttttttaa-------ttttctaattcattgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 6
---------gtatgctttggatcttctataaattaattatgtggatgactatccactttgtccattttttttttatttttgtatggtttctatattttt--tagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG
          ||  ||||   || |  |  | ||    || | |          || ||  |   |   ||  | ||||  | || ||||   | ||||   |||| ||||| || ||||| |||||||||||||||||||| || ||||| ||  |||| ||||||||||||
gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttccagctcacttgcttttttcttctgatttcccaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 6
gtatgct--ttggatcttct--------ataaattaat-tatgtggatgac-tatccacttt-gtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG
| ||||   || ||  || |         ||  || |  |||  |||| || || ||  |   |  || ||  |  ||  || || ||    || |  |||   |||| ||||| || ||||| |||||||||||||||||||| || ||||| ||  |||| ||||||||||||
gcatgccagttagagtttttctcctggagtattttgacatatagggataacataacctttccagctcacttgctcctttcttctg-atttcctcaaattttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgctttggatcttctataaattaattatgtggatgactatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG
         | |   | | ||| |||  | |    |  |   || |  | ||   ||||||  ||| | |||| || |   ||| | |   |||| ||||| || || || |||||||||||||||||||| |||||||| ||  ||||||||||||| |||
---------gcaagctttttaatttatatcttcttacaaagttcaagatcgt---ttttttcattactcttgt-tgataattat-tctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG

upper sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
-----------------gtatgctttggatcttctataaattaa---ttatgt-ggatgactatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG
                    || |       ||||  |  |      |||| |   ||   ||  ||  |      || |||| | |      ||          || ||| |||||||||| || ||||| |||||||||||||||||||| ||||| || ||  |||| ||||| || |||
gcaaagcatattcctctccttgttcctagctttctgcatctggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG

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|211456112|gb|FL153033.1|FL153033
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCCAG-TGGAACAGA
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCC-AGGTGGACCAGA
EST: gi|211022165|gb|FL153038.1|FL153038
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
EST: gi|211456113|gb|FL153034.1|FL153034
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
EST: gi|211024619|gb|FL153052.1|FL153052
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GC-AATGGCGGCTT
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTT
EST: gi|211456114|gb|FL153035.1|FL153035
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
EST: gi|50333167|gb|CO528293.1|CO528293
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
EST: gi|211022178|gb|FL153051.1|FL153051
EST:     TGGTCTACTGGTCA-CACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GGCCAATGGCGGCTTTATC
genomic: TGGTCTACTG-TCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagG-CCAATGGCGGCTTTATC
EST: gi|211022175|gb|FL153048.1|FL153048
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTNAAAGAAAA                         GCCA-TGGCGGCTTTATCATGAGTGCAAGCCCATA-TCCAGGTGGACCAGA
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCC-ATAATCCAGGTGGACCAGA
EST: gi|211022168|gb|FL153041.1|FL153041
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
EST: gi|32943498|gb|CF048317.1|CF048317
EST:     ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAA                         GCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC
genomic: ATGGTCTACTGTCAACACCTGCTGTATCTGCTGTAATTCGTAAAAGAAAAgtatgctttg ... tattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG
                                       tttctatatttttt  CT-rich tract
                attttttttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttggatcttctataaattaattatgtggatgactatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA