RetrogeneDB ID: retro_pvam_856

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_13689:4940..5570(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF170
• Ensembl ID: ENSPVAG00000013497
• Aliases: None
• Description: ring finger protein 170 [Source:HGNC Symbol;Acc:25358]

Sequence

>retro_pvam_856
AGAACTGGAGTGGCCAAATCTCAGTGTGAAGTTCAAAGTTTGAAAGTGGATATTGATTCAGTCATAGAAAGAGTGAGTGG
CCAAGTACTTGTGACAGTTGTGGTTAGTTTTGTTTTGATTACTACCTGGTATATGCACTTTTCAGAAATGCACATCAAAA
CATCCACCCAGAAAAACAAGAACTAGTATGGATACTTCAGAAACAACTTCAAATGTAACAAGATGCCCCTGCTGCAGCTC
AACAGCAGATCTACACTGACATGTGCTGTCCAATTTGTTTACATCAGGCCTTTGTTCCTGTTGAAACAAACTGTGGAAAT
CTCTTTTGTGATACCTGCATTATTGCATACTGGCAATATAGTTCATGGTCTGGGGCAAGTAGTTGGCCAATCTGTAGACA
AATGATAACTTTACTGCTACCAATATTTGGTAAAAAATGATCAGTCTCAGGATGCTGTAAGATTACAACAAAATATTAAT
GATGATAACTGGAGATTCTCAGGGCAGCCCAAATTTATTATGGAAAGAATTGTGGATCTCCCCACATTACTGAGACATGC
TTTCAGGGAAATGTTTTTAGTTGGAGGCCTTTTCTGGATGTTCCACATCAGGATAATACTATGTTTAATG

Alignment

ORF - retro_pvam_856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.83 %
• Parental protein coverage: 62.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPGMAKYQGEVQSLKLDDDSVIEGISDQVLVAVVVSFALIAT-LVYALFRNAHQNIHPENQELVRVLREQ
          R.G.AK.Q.EVQSLK.D.DSVIE..S.QVLV.VVVSF.LI.T.LVYALFRNAHQNIHPE.QELV..L..Q
Retrocopy RTGVAKSQCEVQSLKVDIDSVIERVSGQVLVTVVVSFVLITT<LVYALFRNAHQNIHPEKQELVWILQKQ

Parental  LQTEQDAPAAARQQFYADMYCPICLHQASFPVETNCGHLFCGTCIIAYWRYGSWLGAISCPICRQTVTLL
          LQ..QDAPAAA.QQ.Y.DM.CPICLHQA..PVETNCG.LFC.TCIIAYW.Y.SW.GA.S.PICRQ..TLL
Retrocopy LQM*QDAPAAAQQQIYTDMCCPICLHQAFVPVETNCGNLFCDTCIIAYWQYSSWSGASSWPICRQMITLL

Parental  LPVFG-ENDQSQDAVRLHQDINDYNRRFSGQPRSIMERIMDLPTLLRHAFREMFSVGGLFWMFRIRIILC
          LP.FG..NDQSQDAVRL.Q.IND.N.RFSGQP..IMERI.DLPTLLRHAFREMF.VGGLFWMF.IRIILC
Retrocopy LPIFG>KNDQSQDAVRLQQNINDDNWRFSGQPKFIMERIVDLPTLLRHAFREMFLVGGLFWMFHIRIILC

Parental  LM
          LM
Retrocopy LM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_856 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001127	1 retrocopy	retro_meug_862,
Monodelphis domestica	ENSMODG00000010090	1 retrocopy	retro_mdom_197,
Mus musculus	ENSMUSG00000013878	1 retrocopy	retro_mmus_2907,
Otolemur garnettii	ENSOGAG00000007925	1 retrocopy	retro_ogar_2905,
Pteropus vampyrus	ENSPVAG00000013497	1 retrocopy	retro_pvam_856 ,
Sorex araneus	ENSSARG00000006471	1 retrocopy	retro_sara_706,
Sarcophilus harrisii	ENSSHAG00000018446	1 retrocopy	retro_shar_118,