RetrogeneDB ID: retro_amel_1798

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194384.1:61244..61532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC5L
• Ensembl ID: ENSAMEG00000016540
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5-like [Source:HGNC Symbol;Acc:23366]

Sequence

>retro_amel_1798
ATGGCCCGGAATACACTGTCTTTGCGCTTCCTTCGGGTGGACATCTATCAGTTTGACGAGAAAAAATTCGTGGACCAGCA
GGAGGTTGTGGCAGCGGCGGTGGCCTAGCCACGCCCAGACCCTAGCAAGGTGGACGGCCTTCTGCGGCAAGGGGATATGC
TTCGGGTATTCCATGCAGCCTTACGGAACTCTCCCGTCAACACCAAGAATCAAGCCGTGAAAGAACAAGCCCAACACGTG
GTGCCGAAAGTGCTTACAAACTTTAAGAGTGAGCAGGCTGTGCAGTCA

Alignment

ORF - retro_amel_1798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.8 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARNTLSSRFRRVDIDEFDENKFVDEQEEAAAAAAEPGPDPSEVDGLLRQWDMLRAFHAALRNSPVNTKN
          MARNTLS.RF.RVDI..FDE.KFVD.QE..AAA.A.P.PDPS.VDGLLRQ.DMLR.FHAALRNSPVNTKN
Retrocopy MARNTLSLRFLRVDIYQFDEKKFVDQQEVVAAAVA*PRPDPSKVDGLLRQGDMLRVFHAALRNSPVNTKN

Parental  QAVKERAQGVVLKVLTNFKSSEIEQAVQS
          QAVKE.AQ.VV.KVLTNFKS...EQAVQS
Retrocopy QAVKEQAQHVVPKVLTNFKS---EQAVQS

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_1798 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1798 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016540	1 retrocopy	retro_amel_1798 ,
Callithrix jacchus	ENSCJAG00000006730	4 retrocopies	retro_cjac_1282, retro_cjac_1725, retro_cjac_2744, retro_cjac_3941,
Felis catus	ENSFCAG00000028753	1 retrocopy	retro_fcat_1316,
Macaca mulatta	ENSMMUG00000020628	2 retrocopies	retro_mmul_1650, retro_mmul_623,
Mustela putorius furo	ENSMPUG00000013924	1 retrocopy	retro_mputfur_1532,
Oryctolagus cuniculus	ENSOCUG00000002997	1 retrocopy	retro_ocun_518,
Procavia capensis	ENSPCAG00000013936	1 retrocopy	retro_pcap_274,
Pan troglodytes	ENSPTRG00000021362	1 retrocopy	retro_ptro_2185,
Rattus norvegicus	ENSRNOG00000014317	1 retrocopy	retro_rnor_2730,
Ictidomys tridecemlineatus	ENSSTOG00000007907	2 retrocopies	retro_itri_275, retro_itri_767,
Tupaia belangeri	ENSTBEG00000008398	1 retrocopy	retro_tbel_442,