RetrogeneDB ID: retro_pvam_827

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_12706:18933..19236(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMAT2
• Ensembl ID: ENSPVAG00000009717
• Aliases: None
• Description: zinc finger, matrin-type 2 [Source:HGNC Symbol;Acc:26433]

Sequence

>retro_pvam_827
ATGAAATCGAGCAGCGGGATAAAAAACTTGGACTTTCGCCGAAAGTGAGACAAAGATGAATATGAGAAGCTCACTGAGAA
GAGGCTCATGGAAGAGAGAGAATAGAAGGATGGAAAACCGGTGCACCCGGTCAAGTGGGAGCTTCTCTGGCATAGGGACT
AGAAGGTGGACTTGGAATCCAAACTTGGAAAGACCATTGTCATTACCAAGAGCACTCCACAATCTGAAATGGGAGGATAT
TACTGCAATGTCTGTGACTGTATTGTGAAGGACTCCATCAACTTCCTAGATCACATTAATGGG

Alignment

ORF - retro_pvam_827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.13 %
• Parental protein coverage: 50.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGSGTKNLDFRRKWDKDEYEKLAEKRLTEEREKKDGKPVQPVKRELLRHRDYKVDLESKLGKTIVITK
          M.S.SG.KNLDFRRK.DKDEYEKL.EKRL.EERE.KDGKPV.PVK.ELL.HRD.KVDLESKLGKTIVITK
Retrocopy MKSSSGIKNLDFRRK*DKDEYEKLTEKRLMEERE*KDGKPVHPVKWELLWHRD*KVDLESKLGKTIVITK

Parental  TTPQSEMGGYYCNVCDCVVKDSINFLDHING
          .TPQSEMGGYYCNVCDC.VKDSINFLDHING
Retrocopy STPQSEMGGYYCNVCDCIVKDSINFLDHING

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_827 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 9 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005907	1 retrocopy	retro_cfam_822,
Callithrix jacchus	ENSCJAG00000016231	3 retrocopies	retro_cjac_1137, retro_cjac_1472, retro_cjac_4007,
Dipodomys ordii	ENSDORG00000014559	8 retrocopies	retro_dord_123, retro_dord_127, retro_dord_129, retro_dord_131, retro_dord_133, retro_dord_135, retro_dord_136, retro_dord_138,
Echinops telfairi	ENSETEG00000005406	2 retrocopies	retro_etel_156, retro_etel_882,
Ficedula albicollis	ENSFALG00000008988	1 retrocopy	retro_falb_9,
Myotis lucifugus	ENSMLUG00000017525	2 retrocopies	retro_mluc_2281, retro_mluc_2309,
Monodelphis domestica	ENSMODG00000011269	1 retrocopy	retro_mdom_1209,
Pteropus vampyrus	ENSPVAG00000009717	1 retrocopy	retro_pvam_827 ,
Tursiops truncatus	ENSTTRG00000001777	4 retrocopies	retro_ttru_1889, retro_ttru_340, retro_ttru_721, retro_ttru_766,