RetrogeneDB ID: retro_amel_221

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192356.1:1540072..1540420(-)
• Located in intron of: ENSAMEG00000015654

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSAMEG00000001576
• Aliases: None
• Description: None

Sequence

>retro_amel_221
ATGGCTGAGCTAATCCAGAAGAAGCTACAGGAAAAAGGGGAGAAACAGCAGCAGCTACAGAAGGTCTTGAGTAAATCCAT
GTCAAGGCAGCAGAAGCTTGAGGTGTGACTAACAGAAAGTAATATTGTGAAGGAGGAGTTGGCCCTTTTAGATGGGTCCA
ACATGGTCTTTAAACTTCTGGGTCCTGTGCTGATCAAACAGGAGCTGGGAGAGGCTCAGGCCACAGTGGAGAAGAGGTTG
GACTATATCACAGCTGAAATTAAGTGATATGAATCCCAGCTCTGGGACCTCGAAGGGCAGTCAGAGCAACAGAGGGAGAC
CCTGGCTCAGCTACAGCAGGAGTTCCAG

Alignment

ORF - retro_amel_221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
          MAELIQKKLQ...EK.QQLQK.LSKSMS..QKLE..LTE.NIVKEELALLDGSN.VFKLLGPVL.KQELG
Retrocopy MAELIQKKLQEKGEKQQQLQKVLSKSMSRQQKLEV*LTESNIVKEELALLDGSNMVFKLLGPVLIKQELG

Parental  EARATVGKRLDYITAEIKRYESQLRDLEQQSEQQRETLAQLQQEFQ
          EA.ATV.KRLDYITAEIK.YESQL.DLE.QSEQQRETLAQLQQEFQ
Retrocopy EAQATVEKRLDYITAEIK*YESQLWDLEGQSEQQRETLAQLQQEFQ

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_221 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_221 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 17 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221 , retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Canis familiaris	ENSCAFG00000000956	2 retrocopies	retro_cfam_1749, retro_cfam_1981,
Cavia porcellus	ENSCPOG00000019520	1 retrocopy	retro_cpor_570,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Felis catus	ENSFCAG00000028199	1 retrocopy	retro_fcat_1784,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mustela putorius furo	ENSMPUG00000002364	1 retrocopy	retro_mputfur_608,
Mus musculus	ENSMUSG00000024309	1 retrocopy	retro_mmus_1930,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Pteropus vampyrus	ENSPVAG00000001910	1 retrocopy	retro_pvam_391,
Rattus norvegicus	ENSRNOG00000000473	2 retrocopies	retro_rnor_2216, retro_rnor_2869,
Sorex araneus	ENSSARG00000006330	2 retrocopies	retro_sara_338, retro_sara_453,
Tupaia belangeri	ENSTBEG00000013280	1 retrocopy	retro_tbel_454,