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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCAGGAACGGGAGGGACGATGACGACATGGTCCTCTGGTTCCTAAAGGACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctctaattcactcgtaccagtgaagctcacacctaatagcttctttactcgctcaataatttcctggtatttttttgacgaaggggcgaagcccc...

Basic information

species Zea mays
transcript GRMZM2G156218_T02
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156218_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g21630.1 (Oryza sativa), 5'ss of exon 2
GGGCAGGAACGGGAGGGACGATGACGACATGGTCCTCTGGTTCCTAAAGGACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctctaattcactcgtaccagtgaagc-tcacacctaatagcttctttactcgctcaataatttcctggtatttttttgacgaaggggcgaagcccc---
|||||||||||||||||| ||||| || ||| ||||||||||| | |||||| | ||| |||||||||||||| | || || || || |||||||| || |||||||  ||      |  ||  | |||   | |||   |     ||| |    || | |||  | |  |  ||   | |||           |    |    
GGGCAGGAACGGGAGGGATGATGAGGAGATGATCCTCTGGTTCTTGAAGGACAGGAAGCTCTCCGTCGATGAAACAGTTTCTAAACTGACCAAGGCCATTgtatcctacaaactgtgctgacatgagaaatatgacattca----tttcctgttacgataaatgctcttgttttagcctattgtttcgttcataattttcttta
















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|71420465|gb|DR805107.1|DR805107
EST:     ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATC                         AAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
genomic: ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctcta ... actgcattagAAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
EST: gi|211323100|gb|FL366933.1|FL366933
EST:     ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATC                         AAATGGCGTCATGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
genomic: ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctcta ... actgcattagAAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
EST: gi|71445380|gb|DR826430.1|DR826430
EST:     ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATC                         AAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
genomic: ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctcta ... actgcattagAAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
EST: gi|148937334|gb|EC881515.2|EC881515
EST:     ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATC                         AAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
genomic: ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctcta ... actgcattagAAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
EST: gi|211253175|gb|FL345473.1|FL345473
EST:     ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATC                         AAATGGCGTCATGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
genomic: ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctcta ... actgcattagAAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
EST: gi|71438317|gb|DR819367.1|DR819367
EST:     ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATC                         AAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
genomic: ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctcta ... actgcattagAAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
EST: gi|71445381|gb|DR826431.1|DR826431
EST:     ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATC                         AAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA
genomic: ACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctcta ... actgcattagAAATGGCGTTAGGACTTTGGTGTTGCAGAGTTATCAGAGGAATCAGTGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCAGGAACGGGAGGGACGATGACGACATGGTCCTCTGGTTCCTAAAGGACCGCAAGTTCTCCGTCGATGAAGCCGTCTCCAAGCTCACCAAGGCGATCgtatcctctaattcactcgtaccagtgaagctcacacctaatagcttctttactcgctcaataatttcctggtatttttttgacgaaggggcgaagcccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA