RetrogeneDB ID: retro_amel_489

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192472.1:2431589..2432334(-)
• Located in intron of: ENSAMEG00000004311

Retrocopy information

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

Parental gene information

• Parental gene symbol: YIPF5
• Ensembl ID: ENSAMEG00000010135
• Aliases: None
• Description: Yip1 domain family, member 5 [Source:HGNC Symbol;Acc:24877]

Sequence

>retro_amel_489
ATGTCAGACTTGGATAACATAAACATGGATTTCTACCAGACATGTCACAGCGTTGATGACCAGTCACAGTGGTCCTATGA
TGATGGAGGAAGTGGAGGACCCTATAGCAAATAGGATGCTGGCTAGGATTACTCGCAGCAAGGCCGATTTGTCCCTTCAG
ACATGATACAGCCACAAGAGCCATACACTGGGCTGATTTTCAGCCAACTCAGGTGTACATTCCGACACACGGGCCATTCT
ACGGAAACAACTTTGAGGATGAGCCACCTTTATGAGAAGAATTAGGTATCAATTTTGACCACATCTGGCAAAAACCATGA
ACAGTGTTACAGCCATTAGAAGTAACAGAGAGCAGCATCATGCATGAGACTGAAGTGGCTGGACCAATGGTTTTTTGCCT
TCCCTTCGGGGCCACATTGTTACCAGCTAGCAAAATCCAGTTTGGCTATGTATATGGGATCAGTACAAGTGGATGTCTAG
GAATGTTTTGTTTATTAACTTAATGAGTATGACAGGTGTTTCATTCGGTTATGTGGCAAGTGTCCTTGGATATTGTCTTC
TTCCCATGATCCTACTTTCCAGCTTTACGGTGATATTTTCTTTGTAAGGAATGGTAGGAATCATTATCACTGCTGGAATT
ATTGAATGGTGTAGTTTTTCTGCATCCAAAATTTTTATTTCTGCATTAGCCATGGAAGGATGGCAATTTCTAGTAGCATA
TCCTTGTACTTTGTTATACAGTCTT

Alignment

ORF - retro_amel_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.16 %
• Parental protein coverage: 97.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGFDNLNTDFYQTSYSIDDQSQQSYDYGGSGGPYSKQYAGYDYSQQGRFVPPDMMQPQQPYTGQIF-QP
          M...DN.N.DFYQT..S.DDQSQ.SYD.GGSGGPYSK..AG.DYSQQGRFVP.DM.QPQ.PYTG.IF.QP
Retrocopy MSDLDNINMDFYQTCHSVDDQSQWSYDDGGSGGPYSK*DAG*DYSQQGRFVPSDMIQPQEPYTGLIF<QP

Parental  AQAYTPTTPQPFYGNNFEDEPPLLEELGINFDHIWQKTLTVLHPLKVADGSIMNETDLAGPMVFCLAFGA
          .Q.Y.PT...PFYGNNFEDEPPL.EELGINFDHIWQK..TVL.PL.V...SIM.ET..AGPMVFCL.FGA
Retrocopy TQVYIPTHG-PFYGNNFEDEPPL*EELGINFDHIWQKP*TVLQPLEVTESSIMHETEVAGPMVFCLPFGA

Parental  TLLLAGKIQFGYVYGISAIGCLGMFCLL-NLMSMTGVSFGYVASVLGYCLLPMILLSSFAVIFSLQGMVG
          TLL.A.KIQFGYVYGIS..GCLGMFCLL.NLMSMTGVSFGYVASVLGYCLLPMILLSSF.VIFSL.GMVG
Retrocopy TLLPASKIQFGYVYGISTSGCLGMFCLL<NLMSMTGVSFGYVASVLGYCLLPMILLSSFTVIFSL*GMVG

Parental  IILTAGIIGWCSFSASKIFISALAMEGQQLLVAYPCALLYGV
          II.TAGII.WCSFSASKIFISALAMEG.Q.LVAYPC.LLY..
Retrocopy IIITAGIIEWCSFSASKIFISALAMEGWQFLVAYPCTLLYSL

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_489 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_489 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010135	1 retrocopy	retro_amel_489 ,
Dasypus novemcinctus	ENSDNOG00000014497	1 retrocopy	retro_dnov_16,
Felis catus	ENSFCAG00000031350	1 retrocopy	retro_fcat_177,
Myotis lucifugus	ENSMLUG00000011143	3 retrocopies	retro_mluc_2549, retro_mluc_521, retro_mluc_750,
Otolemur garnettii	ENSOGAG00000001543	2 retrocopies	retro_ogar_2657, retro_ogar_2803,
Tarsius syrichta	ENSTSYG00000008071	1 retrocopy	retro_tsyr_16,