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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcctttgttcaccatgctgctgcgatgtaaacttagtaagcttgttataaagtttctctgtggtccttaactgtttcattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA

Basic information

species Zea mays
transcript GRMZM2G141587_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 10
gttgcctttgttcaccatgctgctgcgatgtaaacttagtaagcttgttataaagtttctctgtggtccttaactgtttcattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA
|||  ||| ||||||||||||  |  | || ||||||    |  || |||||    || | |      || | ||||| ||||||| |||| ||||||||||| || ||||| ||||  |||||||||||||||| |||||| ||||||||||||
gttttctt-gttcaccatgctaatatgttgaaaacttgtatactttcttatacgtcttgttta-----ctaacctgttccatttttcagATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 1
gttgcctttgttcaccatgctgctgcgatgtaaacttagtaagcttgttataaagtttctctgtggtccttaactgtttcattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA
|||   | |||||||||||||  |  | || ||||||   |  |||  |   | ||     |    |||| | |||||  |||||| |||| ||||||||||| || ||||| || || |||||||||||||||| |||||| ||||||||||||
gtt--ttctgttcaccatgctaatatgttgaaaacttgtaatactttcttatacgtcatgtt----tcctaacctgttctatttttcagATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 10
------------------gttgcctttgttcaccatgctgctgcg-atgtaaacttagtaagcttgttataa--agtttctctgtggtccttaact--gtttcat------tttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA
                  |  |  ||  |       ||||    | |||  ||  || |     | || |      ||| |||    |  | || |  ||  |||      || | || |  ||||||| ||  | || || ||||| ||||| |||||||||| ||||||||||||||| |||
gtttatttccctacatgtgcagatttcatctttttggctgagatggatgagaaactattttttctcttctttttgctttgtctaacatagtcaatttggtaacatctattattctcagGTTACAGATGGAGAAAGATTGCCTTTGGCTGTGAAAGAGTTGGGAACCTGTGACCTTTATCCTCAA

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|60341035|gb|DN208008.1|DN208008
EST:     ATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAG                         ATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAGgttgcctttg ... cattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGT
EST: gi|93016009|gb|EB641529.1|EB641529
EST:     ATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAG                         ATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAGgttgcctttg ... cattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGT
EST: gi|32928123|gb|CF032935.1|CF032935
EST:     ATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAG                         ATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGT
genomic: ATAATGAAATCCAAACTGTTAATATCAAGAGTGTTGGTGCAGACAATGAGgttgcctttg ... cattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagtaagcttgttataaagtttctctgtggtccttaactgtttcattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA
                                 ccttaac  putative branch site (score: 3)
                                       ctgtttcatttttt  CT-rich tract
          ttgttataaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcctttgttcaccatgctgctgcgatgtaaacttagtaagcttgttataaagtttctctgtggtccttaactgtttcattttttagATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG