RetrogeneDB ID: retro_amel_242

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192364.1:3966729..3967177(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OIP5
• Ensembl ID: ENSAMEG00000016777
• Aliases: None
• Description: Opa interacting protein 5 [Source:HGNC Symbol;Acc:20300]

Sequence

>retro_amel_242
AGGTGTCAATGCGCACAGTGCCACACTGTGCACGTAGCATGGGACACATCATGGTCCCTCAGGTCTGTGGTCTAATCCAG
AGTCACAAGTAACGTGGTTTGGGAAGCTCCCTTCCTAGTTGGGATTGAAGGCTTGTTCAAAGGCAGCACTTAAAACTTTT
TATTCTGTACTTCCTATGGGATTGCCATTGGTTTCCATTTGTATTCTACCCATGCCACCCTGGCTGCCTTCTGAGGTCAC
TTCTGCCTTTCCGGTGACAAAATGGTGTGCTATCTCTTAAAAACAAAAGCTACAGCAAATGCATCTGAGATGGATATTCA
CAACTTCTTTCTACCAGAAAAGATTGCAGAGCCTGAAAGAGAAGATAATATTAACAACACCTACTAACTTAAATTCATGG
ATGAAGATTCTGAAGTAAGTAACTCCTGACCAGCCCAAGCCAGAAAAC

Alignment

ORF - retro_amel_242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.67 %
• Parental protein coverage: 64.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QCYAVLADSVHLAWDLARSLGAVVFSRVTNNVVLEAPFLVGIEGSLKGSTYNLLFCTSCGISIGFHLYST
          .C.......VH.AWD...SL..VV.SRVT.NVV.EAPFLVGIEG..KGST.N.LFCTS.GI.IGFHLYST
Retrocopy RCQCAQCHTVHVAWDTSWSLRSVV*SRVTSNVVWEAPFLVGIEGLFKGST*NFLFCTSYGIAIGFHLYST

Parental  HAALAALRGHFCLSSDKMVCYLLKTKAIVSASEMDIHNLSLPEKVAE-LKEKIML-THTHLHSLMKILKE
          HA.LAA..GHFCLS.DKMVCYLLKTKA...ASEMDIHN..LPEK.AE.LKEKI.L.T.T.L.S.MKILK.
Retrocopy HATLAAF*GHFCLSGDKMVCYLLKTKATANASEMDIHNFFLPEKIAE>LKEKIILTTPTNLNSWMKILK*

Parental  VTPDQPKPEN
          VTPDQPKPEN
Retrocopy VTPDQPKPEN

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_242 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_242 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016777	1 retrocopy	retro_amel_242 ,
Bos taurus	ENSBTAG00000010766	1 retrocopy	retro_btau_1700,
Felis catus	ENSFCAG00000030520	1 retrocopy	retro_fcat_1387,
Myotis lucifugus	ENSMLUG00000009765	2 retrocopies	retro_mluc_2106, retro_mluc_2341,
Mustela putorius furo	ENSMPUG00000008828	2 retrocopies	retro_mputfur_1518, retro_mputfur_1534,
Otolemur garnettii	ENSOGAG00000033746	1 retrocopy	retro_ogar_1761,
Sorex araneus	ENSSARG00000009593	2 retrocopies	retro_sara_351, retro_sara_629,