RetrogeneDB ID: retro_amel_1846

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194780.1:106457..107037(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000003197
• Aliases: None
• Description: None

Sequence

>retro_amel_1846
TCTTTCCTCTTTGCCCTTGAAAATCTGCCGGCATCCCAAAATTCCCATTGTGCATCAGGCTGGCATGTTGACATGAAATT
GTTTTGCCTCTGTCTTTGAAAAATACTCCCAATTGCAAGAAAAGGGCAAGGAAAGAGAGAACGGGGCAGTTATCCATTAG
AGGGATGATGAGACCATGTCTGTTGGGTCTAAGAGGACAGAGCCACAGTAATCTTCAGCACAGTGTTTAAGGGTGACGAC
GCCGTAGTCTTTGGAAAAGTGTTCACGCAGGAGTACAAAGAAGGACACAGAGCCAGCCGCACAGCCCCACAGGTCCCCTG
TAGCCACCGGAAACCTCCTCTGGTGCTGAAAGACACGGATGCCGCAGCGGGTGGCAACACTGGCTCTATGACCTTCGTGC
TATTCCCTCGCCACACCAATGCCAGTGCTCGAGATAACACCACGGACCTGACCCACACGTTCCGGGACCGCCTGAACGAG
CACATTGAGTGCTCTAAGGCCTAGATGCACACACGATGGGGGCAAAAACAGCGACTTCCTCAAGGTGCTGAATGGTGCAC
GCCCAGATGCCGAGAAAAGA

Alignment

ORF - retro_amel_1846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.75 %
• Parental protein coverage: 55.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SLLYDLENLPASKDS-IVHQAGMLKRNCFASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKK-DRV
          S.L..LENLPAS..S.IVHQAGML..NCFASVFEKY.Q.QE.GKE.EN.AVIH.RDDETM.V.SK..DR.
Retrocopy SFLFALENLPASQNS>IVHQAGMLT*NCFASVFEKYSQLQEKGKERENGAVIH*RDDETMSVGSKR<DRA

Parental  TVVFSTVFKDDDDVVIGKVFMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRH
          TV.FSTVFK.DD.VV.GKVF.QE.KEG.RAS.TAPQV..SHR.PPL.LKDTDAA.G.N.G..TFVLFPRH
Retrocopy TVIFSTVFKGDDAVVFGKVFTQEYKEGHRASRTAPQVPCSHRKPPLVLKDTDAAAGGNTGSMTFVLFPRH

Parental  TNASARDNTINLIHTFRDYLHYHIKCSKAYIHTR-MRAKT-SDFLKVLNRARPDAEKK
          TNASARDNT..L.HTFRD.L..HI.CSKA..HTR.M.AKT.SDFLKVLN.ARPDAEK.
Retrocopy TNASARDNTTDLTHTFRDRLNEHIECSKA*MHTR<MGAKT<SDFLKVLNGARPDAEKR

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_1846 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1846 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003197	2 retrocopies	retro_amel_1771, retro_amel_1846 ,
Canis familiaris	ENSCAFG00000014618	1 retrocopy	retro_cfam_513,
Choloepus hoffmanni	ENSCHOG00000010564	5 retrocopies	retro_chof_1845, retro_chof_2103, retro_chof_2226, retro_chof_2227, retro_chof_473,
Dasypus novemcinctus	ENSDNOG00000006037	1 retrocopy	retro_dnov_5,
Dipodomys ordii	ENSDORG00000016107	1 retrocopy	retro_dord_624,
Felis catus	ENSFCAG00000002370	1 retrocopy	retro_fcat_732,
Loxodonta africana	ENSLAFG00000007414	1 retrocopy	retro_lafr_593,
Myotis lucifugus	ENSMLUG00000004161	1 retrocopy	retro_mluc_390,
Mustela putorius furo	ENSMPUG00000016512	1 retrocopy	retro_mputfur_1294,
Mus musculus	ENSMUSG00000006304	1 retrocopy	retro_mmus_1556,
Oryctolagus cuniculus	ENSOCUG00000005516	1 retrocopy	retro_ocun_483,
Pteropus vampyrus	ENSPVAG00000017133	1 retrocopy	retro_pvam_1216,
Sorex araneus	ENSSARG00000003326	1 retrocopy	retro_sara_283,
Tarsius syrichta	ENSTSYG00000001037	1 retrocopy	retro_tsyr_557,