RetrogeneDB ID: retro_zmay_49

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 2:11824433..11825564(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G368398
• Aliases: None
• Description: None

Sequence

>retro_zmay_49
TACAAGTTGACCTATCCAAGTGGCACAGCCACTGCATATCTCATCAACGGTTTTCACACACCTGAGGGAGCCAAGCTTGC
AAAGAAGCAAGTAAAGACGTTGGGCAAGTACTTCGTGTTTAGCTTTTTCTGGGGCTTTTTTCAGTGGTTCTACACTGCAG
GGGATGAGTGTGGATTCAAAAATTTCCCAACATTGGGCCTTGAAGCTTATAACAATAGGTTCTTCTTTGACTTCTCTCCT
ACTTACGTTGGAGTTGGCATGATCTGCCCATACATCGTGAATGTGTCTGTTCTGCTGGGTGGTATCCTCTCATGGGGTTT
AATGTGGCCTCTCATTGCCAAGAAGAAGGGGAGTTGGTACCCAGCTAACCTGGAAGACTCAAGTTTACATGGGTTGCAGG
CTTATAGGGTTTTCATTTCCATCGCTTTGATCCTTGGGGACGGTTTATACAACTTCATTAAGGTGCTGATCCGCACAATT
GCGGGTTTCATATCAATGGTGCAGGTGCAGCAAAATTCAAAAAGCATGCTTCCTGTTTCGGACAATGGCAGTTCCATGTC
CAGTACGGAGGCTGTATCCTTTGACGATGAACGTCGCATCGAGAATTTTCTAAAAGACCAGATTCCCAAGTCAGTTGCAT
ACGGGGGCTATGTTGCAGTTGCTGCTATATCTATTGGCACCCTTCCTCAGATCTTCCTGCAACTCAAGTGGTACTACATT
TTAGTAGCCTGCGTCGTGGCACCTGTGCTGGCCTTCTGCAATGCTTATGGAAGTGGCCTCACTGACTGGTCTCTCGCCTC
CACCTACGACAAGCTCGCTATCTTCGTGTTCGGTGCATGGGCTGGCCTCTCACACGGTGGCGTGCTCGTTGGGCTCGCAA
CTTATGGTGTCATGATGAGCATCGTGTCGACCACCTCAGACCTGATGCAAGACTTCAAGACCGGGTACCTGACGCTGGCG
TCACCGAGGTCTATGTTCATCAGCCAGGTGATTGGCACCGGGATGGGGTGTGTCATCGGGCCCTGCATCTTCTGGCTCTT
CTACAAGGCGTTCGGTGACATTGGCGAGAGCGGCACCGAGTACCCGGCGCCCTATGCCATCGTGGTACTGAATGATGTCT
TGGTACAGATA

Alignment

ORF - retro_zmay_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.49 %
• Parental protein coverage: 52.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YKLTYPSGTATAYLINGFHTPEGAKLAKKQVKTLGKYFVFSFFWGFFQWFYTAGDECGFKNFPTLGLEAY
          YKLTYPSGTATAYLINGFHTPEGAKLAKKQVKTLGKYFVFSFFWGFFQWFYTAGDECGFKNFPTLGLEAY
Retrocopy YKLTYPSGTATAYLINGFHTPEGAKLAKKQVKTLGKYFVFSFFWGFFQWFYTAGDECGFKNFPTLGLEAY

Parental  NNRFFFDFSPTYVGVGMICPYIVNVSVLLGGILSWGLMWPLIAKKKGSWYPANLEDSSLHGLQAYRVFIS
          NNRFFFDFSPTYVGVGMICPYIVNVSVLLGGILSWGLMWPLIAKKKGSWYPANLEDSSLHGLQAYRVFIS
Retrocopy NNRFFFDFSPTYVGVGMICPYIVNVSVLLGGILSWGLMWPLIAKKKGSWYPANLEDSSLHGLQAYRVFIS

Parental  IALILGDGLYNFIKVLIRTIAGFISMVQ--QNSKSMLPVSDNGSSMSSMEAVSFDDERRIENFLKDQIPK
          IALILGDGLYNFIKVLIRTIAGFISMVQ..QNSKSMLPVSDNGSSMSS.EAVSFDDERRIENFLKDQIPK
Retrocopy IALILGDGLYNFIKVLIRTIAGFISMVQVQQNSKSMLPVSDNGSSMSSTEAVSFDDERRIENFLKDQIPK

Parental  SVAYGGYVAVAAISIGTLPQIFPQLKWYYILVAYVVAPVLAFCNAYGSGLTDWSLASTYGKLAIFVFGAW
          SVAYGGYVAVAAISIGTLPQIF.QLKWYYILVA.VVAPVLAFCNAYGSGLTDWSLASTY.KLAIFVFGAW
Retrocopy SVAYGGYVAVAAISIGTLPQIFLQLKWYYILVACVVAPVLAFCNAYGSGLTDWSLASTYDKLAIFVFGAW

Parental  AGLSHGGVLVGLAACGVMMSIVSTASDLMQDFKTGYLTLASPRSMFISQVIGTGMGCVIGPCIFWLFYKA
          AGLSHGGVLVGLA..GVMMSIVST.SDLMQDFKTGYLTLASPRSMFISQVIGTGMGCVIGPCIFWLFYKA
Retrocopy AGLSHGGVLVGLATYGVMMSIVSTTSDLMQDFKTGYLTLASPRSMFISQVIGTGMGCVIGPCIFWLFYKA

Parental  FGDIGESGTEYPAPYAIVYRNMAILGV
          FGDIGESGTEYPAPYAIV..N......
Retrocopy FGDIGESGTEYPAPYAIVVLNDVLVQI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Zea mays was not studied using RNA-Seq expression data.

ChIP-Seq

Zea mays was not studied using ChIP-Seq data.

EST

Zea mays was not studied using EST data.

TSS

Zea mays was not studied using FANTOM5 data.

Lab

retro_zmay_49 was not experimentally validated.

Homology

Retrocopy orthology:

Zea mays does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G368398	2 retrocopies	retro_zmay_32, retro_zmay_49 ,