RetrogeneDB ID: retro_meug_2041

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold82759:243..635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDA
• Ensembl ID: ENSMEUG00000016075
• Aliases: None
• Description: cytidine deaminase [Source:HGNC Symbol;Acc:1712]

Sequence

>retro_meug_2041
CCAATTAAGATGAAGCAGCTCATTTGCCGGAGTCAAGAGGCCAAGGAGTTTGCCTACTGTCCCTACAGTAACTTCCCAGT
GAGATCAGCTCTTCTGACTCTGAATGGGAAGATTTTTTTTCAGATGCAATTTAGGAAATGCTGCCTACCCACTAGGCATA
TGGATAGAATGCACTGCCATTCAGAAGGCCATGTCAGAAGGACACAAAGAGTTCTGGGCCATTGCTATTACCAGTAATTT
GGAGAATGACTTTATCCCACTATCTGGAGCCTGTAGACAAGTAATGAGAGAGGTTCAAAAACATTGGCCTGTCTACATGA
CAAAAAGCAGATGGTACATATGATGTCAGGATGGTCCATGAATCATTTGAACCAGATGACCTGCAGAAGTCC

Alignment

ORF - retro_meug_2041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.85 %
• Parental protein coverage: 91.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKNQQQLICKGQEAKEFAYCPYSNFPVGAALLTLDGKIFSG-CNVENAAYPVGTCAERTAIQKAISEGHK
          P....QLIC..QEAKEFAYCPYSNFPV..ALLTL.GK.....CN..NAAYP.G...E.TAIQKA.SEGHK
Retrocopy PIKMKQLICRSQEAKEFAYCPYSNFPVRSALLTLNGKXXXQ>CNLGNAAYPLGIWIECTAIQKAMSEGHK

Parental  QFRAIAITSNTENNFIIPFGACRQVMREFGKHWYVYMT-KADGTYEVKMVHELLPASFGPDDLQKN
          .F.AIAITSN.EN.FI...GACRQVMRE..KHW.VYMT.KADGTY.V.MVHE....SF.PDDLQK.
Retrocopy EFWAIAITSNLENDFIPLSGACRQVMREVQKHWPVYMT>KADGTYDVRMVHE----SFEPDDLQKS

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_2041 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2041 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011900	1 retrocopy	retro_dord_61,
Macropus eugenii	ENSMEUG00000016075	6 retrocopies	retro_meug_102, retro_meug_1601, retro_meug_1617, retro_meug_2041 , retro_meug_527, retro_meug_603,
Ochotona princeps	ENSOPRG00000007364	2 retrocopies	retro_opri_282, retro_opri_603,