RetrogeneDB ID: retro_amel_1594

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193688.1:205359..205737(+)
• Located in intron of: ENSAMEG00000006456

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000002786
• Aliases: None
• Description: None

Sequence

>retro_amel_1594
ATGGCGATGCAAGCAGCCAAGAGGTGGAACGCTCGACTTCCACCTGAAGTAAATTAGATTTTATATATAAGAAATTTACC
ATACAAAATCAAAGCTGAAGAAATGTACGATATATTTGGGAAATATGGGCCTATTCATCAAATCCGAGTGGGAAACACAC
CCGAAACTAGAGGAACAGCTTATGTGGTCTTTGAAGACATCTTTAACGCCAAGAACACACATGATCAACTTGCAGGACTC
AATTTTTGGAACAGATACCTGGTGGTTTTGTACTATAATGCCAACAGCGCATTTCAGAAGATGGACACAAAAAAGAAGGA
AGAGCAGCAGTTGACACTTCTCAGGGAGAAATATGGCATTAACACAGATCCACCGAAA

Alignment

ORF - retro_amel_1594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDA
          MAMQAAKR.N.RLPPEVN.ILYIRNLPYKI.AEEMYDIFGKYGPI.QIRVGNTPETRGTAYVV.EDIF.A
Retrocopy MAMQAAKRWNARLPPEVN*ILYIRNLPYKIKAEEMYDIFGKYGPIHQIRVGNTPETRGTAYVVFEDIFNA

Parental  KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEE-QLKLLKEKYGINTDPPK
          KN..D.L.G.N..NRYLVVLYYNAN.AFQKMDTKKKEE.QL.LL.EKYGINTDPPK
Retrocopy KNTHDQLAGLNFWNRYLVVLYYNANSAFQKMDTKKKEEQQLTLLREKYGINTDPPK

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_1594 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1594 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002786	1 retrocopy	retro_amel_1594 ,
Bos taurus	ENSBTAG00000003407	1 retrocopy	retro_btau_606,
Choloepus hoffmanni	ENSCHOG00000000689	3 retrocopies	retro_chof_1217, retro_chof_2457, retro_chof_351,
Callithrix jacchus	ENSCJAG00000007716	2 retrocopies	retro_cjac_2632, retro_cjac_487,
Dasypus novemcinctus	ENSDNOG00000007148	1 retrocopy	retro_dnov_1313,
Equus caballus	ENSECAG00000015618	1 retrocopy	retro_ecab_733,
Felis catus	ENSFCAG00000031365	1 retrocopy	retro_fcat_247,
Homo sapiens	ENSG00000115128	1 retrocopy	retro_hsap_1773,
Macaca mulatta	ENSMMUG00000001282	1 retrocopy	retro_mmul_1262,
Mustela putorius furo	ENSMPUG00000013957	1 retrocopy	retro_mputfur_882,
Nomascus leucogenys	ENSNLEG00000000815	1 retrocopy	retro_nleu_2806,
Otolemur garnettii	ENSOGAG00000004468	1 retrocopy	retro_ogar_2877,
Pongo abelii	ENSPPYG00000012603	2 retrocopies	retro_pabe_1098, retro_pabe_1461,
Pan troglodytes	ENSPTRG00000011709	1 retrocopy	retro_ptro_1187,
Sorex araneus	ENSSARG00000011902	1 retrocopy	retro_sara_638,