RetrogeneDB ID: retro_amel_602

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192520.1:475039..475835(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACAA2
• Ensembl ID: ENSAMEG00000009411
• Aliases: None
• Description: acetyl-CoA acyltransferase 2 [Source:HGNC Symbol;Acc:83]

Sequence

>retro_amel_602
TCAGATACTATATACTCTGCCTGGAATGTTGGTTTGAGTATAGGTATCTCAAAAGAAACCTCAGCTCTCACCCGTTAATA
AGGTCTGTGGCTCTGTTTTCCAGTCCATTGTGAACCGATATCAGGAAGTTTGTATTTCAGATGCTGAAGCCATATCGTAT
GGAGGAGCTGAAAACATGAGCCGGGTTCCCTACTGTGTCAGAAACACGTGTTTTATAACCAAGTTTGGAAATGCTCTCAA
GCTGGAAGTGTCTTTGTGAGCAACATTAACAGATCAACATGTCCAATTTCCCATTGGAATTACTGCAGAGAATTTTGCTG
CAAAACATAAAGGTAGCAGAGAAGGATGTAACAAATATGCCCTGTAATCACAGCAGAGGTGGATAGCTGCCAATAATGCT
GTGACTTTAATAATGAGATGTTACCTACTGAGGTGAAGACAGAGAAAGGGATACAGGCAGTGCAAGTAGATGATCCTGCT
GGGCTCCAGACAAGCCTGGAACAGTTAAATAAACTTCCTCTAGTATTCACCGAAGAAGGGACGGCTGCTTCAGGGAGTGC
ACTGGGAATATCTGGCACCTTCAAAGCTAGTGAAGTTGCTGGCAAAGAAGCATAACGTCACACCACTGGCAAGAATTATG
GGCTATTTTGTGTCTGGATGTGATCCCTCAATCATGGATATTGGGCTTGTCTCTACTGTCAATGAGGCAGTAAATAAAAC
AAGACTGAATCTTAAGGAGATGGAAATGGTAGAGGTGAATGAAATTTTTGCTCTCTAGTACTTGACAGTGGAGAAG

Alignment

ORF - retro_amel_602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.29 %
• Parental protein coverage: 67.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SDAAYLARHVGLRVGVPKEIPALT-VNRLCGSGFQSIVSGCQEICVKDAEVVLCGGTESMSQSPYCVRNI
          SD..Y.A..VGL..G..KE..ALT.VN..CGS.FQSIV...QE.C..DAE....GG.E.MS..PYCVRN.
Retrocopy SDTIYSAWNVGLSIGISKETSALT>VNKVCGSVFQSIVNRYQEVCISDAEAISYGGAENMSRVPYCVRNT

Parental  RFGTKFGSDLKMEDALWSGLTDEHIRLPMGITAENLAAKHNISREDCDKYALQSQQRWKAANDAGY-FNN
          .F.TKFG..LK.E..L...LTD.H...P.GITAEN.AAKH..SRE.C.KYAL.SQQRW.AAN.A...FNN
Retrocopy CFITKFGNALKLEVSL*ATLTDQHVQFPIGITAENFAAKHKGSREGCNKYAL*SQQRWIAANNAVT<FNN

Parental  EMAPIEVKTKKGKQTMQVDEHARPQTTLEQLHKLPPVFKKEGTVTAGNASGVSDGAGVVIIASEEA-VKK
          EM.P.EVKT.KG.Q..QVD..A..QT.LEQL.KLP.VF..EGT.....ASG...G......ASE.A..KK
Retrocopy EMLPTEVKTEKGIQAVQVDDPAGLQTSLEQLNKLPLVFTEEGTA----ASGSALGISGTFKASEVA>AKK

Parental  HNFTPLARIVGYFVSGCDPSIMGIGPVPAINGALKKTGQSLKDMDLVEVNEAFAPQYLAVEK
          HN.TPLARI.GYFVSGCDPSIM.IG.V...N.A..KT...LK.M..VEVNE.FA..YL.VEK
Retrocopy HNVTPLARIMGYFVSGCDPSIMDIGLVSTVNEAVNKTRLNLKEMEMVEVNEIFAL*YLTVEK

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_602 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_602 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009411	1 retrocopy	retro_amel_602 ,
Equus caballus	ENSECAG00000019394	1 retrocopy	retro_ecab_454,
Homo sapiens	ENSG00000167315	1 retrocopy	retro_hsap_4829,
Gorilla gorilla	ENSGGOG00000012552	1 retrocopy	retro_ggor_3011,
Myotis lucifugus	ENSMLUG00000022960	1 retrocopy	retro_mluc_654,
Nomascus leucogenys	ENSNLEG00000011576	1 retrocopy	retro_nleu_2706,
Ochotona princeps	ENSOPRG00000007567	2 retrocopies	retro_opri_1224, retro_opri_348,
Pan troglodytes	ENSPTRG00000010016	1 retrocopy	retro_ptro_3214,
Vicugna pacos	ENSVPAG00000012121	1 retrocopy	retro_vpac_625,