RetrogeneDB ID: retro_amel_636

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192540.1:864226..864740(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000017318
• Aliases: None
• Description: None

Sequence

>retro_amel_636
GCCACAGAGCTGACGCTGCTGGAGAAGTCCCTGGGGGCTGAGCAAAGAGAACAAACACAGCGCTGATGGTGAGCGCCAGA
TTCCAGTTCTTCAAGCAAACAATGGTCCAAGTCTACCAGGACTGACTACTGTAGCAGCTCATCTTGTCAAGCAGGCCAAC
AAAGAACATTTGCTTGGGAGCACTGCAGAAGAAAAAGCAATCGTTCAGCAGTGGTTGGAATACAAGGTAACTTGAGTAGA
CGGACACTTCAGTAAAGACGATATCCACACTCTGTTGAAGGATCTTAATTCCTATCTTGAAGATAAAGTCTACCTTACAG
GATATAACTTTACCTTAGCAGATATCCTCTTGTACTACAGACTTCATTGCTTTAGAGTTGACCTGACAGTTCAAGAAAAG
GAGGAATATCTTAATGTGTCTCGCTGGTCTTGTCACATTGAACACTACCCAGGGATTGGGCGGCATCTGTCCATTGTTGT
CTTCATCAAGAACAGACTATGTACTAATTCCCAC

Alignment

ORF - retro_amel_636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.63 %
• Parental protein coverage: 98.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAELTLLEKSLG-LSKGNKYSAQGERQFKIPVLQTNNGPSLTGLTTIAAHLVKQANKEHLLGSTAEEKAI
          A.ELTLLEKSLG.LSK.NK.SA.GERQ..IPVLQ.NNGPSL.GLTT.AAHLVKQANKEHLLGSTAEEKAI
Retrocopy ATELTLLEKSLG>LSKENKHSADGERQ--IPVLQANNGPSLPGLTTVAAHLVKQANKEHLLGSTAEEKAI

Parental  VQQWLEYRVTRVDGHSNKDDIRTLLKDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYL
          VQQWLEY.VT.VDGH..KDDI.TLLKDLNSYLEDKVYLTGYNFTLADILLYY.LH.F.VDLTVQEKE.YL
Retrocopy VQQWLEYKVT*VDGHFSKDDIHTLLKDLNSYLEDKVYLTGYNFTLADILLYYRLHCFRVDLTVQEKEEYL

Parental  NVSRWFCHIQHYPGIRQHLSVVVFIKNRLYTNSH
          NVSRW.CHI.HYPGI..HLS.VVFIKNRL.TNSH
Retrocopy NVSRWSCHIEHYPGIGRHLSIVVFIKNRLCTNSH

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_636 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_636 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017318	1 retrocopy	retro_amel_636 ,
Dasypus novemcinctus	ENSDNOG00000019203	1 retrocopy	retro_dnov_1550,
Erinaceus europaeus	ENSEEUG00000006156	1 retrocopy	retro_eeur_87,
Felis catus	ENSFCAG00000011622	1 retrocopy	retro_fcat_1075,
Macropus eugenii	ENSMEUG00000008960	1 retrocopy	retro_meug_1883,
Microcebus murinus	ENSMICG00000012636	1 retrocopy	retro_mmur_1404,
Myotis lucifugus	ENSMLUG00000007715	1 retrocopy	retro_mluc_1474,
Mustela putorius furo	ENSMPUG00000000588	1 retrocopy	retro_mputfur_486,
Pteropus vampyrus	ENSPVAG00000012305	2 retrocopies	retro_pvam_1374, retro_pvam_190,
Rattus norvegicus	ENSRNOG00000016390	5 retrocopies	retro_rnor_1682, retro_rnor_2013, retro_rnor_2132, retro_rnor_2133, retro_rnor_785,