RetrogeneDB ID: retro_amel_1758

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194225.1:240876..241465(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLS1
• Ensembl ID: ENSAMEG00000010596
• Aliases: None
• Description: cardiolipin synthase 1 [Source:HGNC Symbol;Acc:16148]

Sequence

>retro_amel_1758
GAGGCCCCAGGCTGACCATGGGGCCTGACAATCACCACCAAGCCTGTGTGAAAATCCACGGACAATTCCACATACCTTGT
CAATGAGAAGAACCAACTTGGCCCCAGTTTGGAGCTATTTGATTACTGGAGAACATTTTGATATTGCACTAGGAGTTTTG
CTCTAGTTGGGATCACTGATTTATTGGGTGGATTTATCGCTTGAAATTGGGACACTTGTTAATCATCTTTGGAAAATATT
CTTGGTCCACTTGCTGATGAAATCCCTATCAGCATCCTCCACGTTAGCTTGACCTATGCAGATCTTACTACAGTTTCACT
TGTTTATACGATAATTTCAAAGATGTAATATTGGTTCCTACCATTTTTATGTCATATATTGAATTCTTCCAACACTGAGA
ACAGTTGCTAAGTATTTCAATTTTTGCTGTGTCACCACTAAATTAAAACCAACATGCACCAGCAATGTAAGCATAGCAGT
CCAGTTAATCTTGGCGGTTTCTTTGGCAGCTCTGGTTTTCAATTATGCTGACAGTATTTATCTTCAGATACTGTGGTGAT
TCATAGTTTGCAGCCCAGCTGCATCAGCT

Alignment

ORF - retro_amel_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.39 %
• Parental protein coverage: 81.48 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EARGGRWGVSTAS-CLYENPWTIPNMLSMTRIGLAPVLGYLIIEEDFNIALGV-FALAGLTDLLDGFIAR
          EA.G..WG.......L.ENP.TIP..LSM.R..LAPV..YLI..E.F.IALGV.FAL.G.TDLL.GFIA.
Retrocopy EAPG*PWGLTITT>SLCENPRTIPHTLSMRRTNLAPVWSYLITGEHFDIALGV<FALVGITDLLGGFIA*

Parental  NWANQKSALGSALDPLADKILISILYVSLTYADLIPVPLTYMIIS-RDVMLIAAV-FYVRYRTLPTPRTL
          NW....S.L...L.PLAD.I.ISIL.VSLTYADL..V.L.Y.IIS..DV.L.....FYV.Y..LPT.RT.
Retrocopy NWDTC*SSLENILGPLADEIPISILHVSLTYADLTTVSLVYTIIS<KDVILVPTI<FYVIY*ILPTLRTV

Parental  SKYFNPCYATARLKPTFISKVNTAVQLILVAASLAAPVFNYADSIYLQILWCFTAFTTAASA
          .KYFN.C..T..LKPT..S.V..AVQLIL.A.SLAA.VFNYADSIYLQILW.F.....AASA
Retrocopy AKYFNFCCVTTKLKPTCTSNVSIAVQLIL-AVSLAALVFNYADSIYLQILW*FIVCSPAASA

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_1758 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1758 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010596	1 retrocopy	retro_amel_1758 ,
Bos taurus	ENSBTAG00000000065	1 retrocopy	retro_btau_1167,
Canis familiaris	ENSCAFG00000005934	1 retrocopy	retro_cfam_1002,
Equus caballus	ENSECAG00000023869	2 retrocopies	retro_ecab_247, retro_ecab_930,
Felis catus	ENSFCAG00000023647	1 retrocopy	retro_fcat_1393,
Microcebus murinus	ENSMICG00000011666	1 retrocopy	retro_mmur_751,
Mustela putorius furo	ENSMPUG00000006349	1 retrocopy	retro_mputfur_1021,
Rattus norvegicus	ENSRNOG00000021273	3 retrocopies	retro_rnor_2865, retro_rnor_2866, retro_rnor_2977,