RetrogeneDB ID: retro_meug_102

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_2502:66086..66528(+)
• 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_102
ATGGCTCAAGTGCCCATTGGTCTGGCAAGGGAACTTCCGATCCAGCCCAGATTAAGCAGCTCATTTGCAAGTGCCAAGAA
GCCAAGGAGTTTGCCTACTGTCTCTATGGTAACTTCCCAGTGTGGCCAGCTCTCCTGATTCTGGACAGAAGATTTTTTCA
GAATGCAACATAGAAAAAGCATTCTACCCAGAAGGCACCTGTGCAGAACACACCACCATTCAGAAGGCCATCTGGGAAGG
ACACAAACAGTTCCAGGCCATTGCTATTACCAGTAATTTGAAGGATGACTTTATTGCACTATGTGGAGCTTGCAGACAAG
TGATGAGAGAGTTTGGAAAACACTGATATGTCCACGTGACACAAACAGATGGCACATATGAACTCAAGATGGTCCATGGA
CTACTTCCTGGATCATGTGGATCAGATGACCTAAAGAAGAAC

Alignment

ORF - retro_meug_102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQAPVGLA-QCP-SPKNQQQLICKGQEAKEFAYCPYSNFPVGAALLTLDG-KIFSGCNVENAAYPVGTC
          MAQ.P.GLA...P..P....QLICK.QEAKEFAYC.Y.NFPV..ALL.LD..KIFS.CN.E.A.YP.GTC
Retrocopy MAQVPIGLARELP<DPAQIKQLICKCQEAKEFAYCLYGNFPVWPALLILDR<KIFSECNIEKAFYPEGTC

Parental  AERTAIQKAISEGHKQFRAIAITSNTENNFIIPFGACRQVMREFGKHWYVYMTKADGTYEVKMVHELLPA
          AE.T.IQKAI.EGHKQF.AIAITSN....FI...GACRQVMREFGKH.YV..T..DGTYE.KMVH.LLP.
Retrocopy AEHTTIQKAIWEGHKQFQAIAITSNLKDDFIALCGACRQVMREFGKH*YVHVTQTDGTYELKMVHGLLPG

Parental  SFGPDDLQKN
          S.G.DDL.KN
Retrocopy SCGSDDLKKN

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_102 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_102 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,