RetrogeneDB ID: retro_pvam_981

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_20494:7238..7832(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH2
• Ensembl ID: ENSPVAG00000003397
• Aliases: None
• Description: malate dehydrogenase 2, NAD (mitochondrial) [Source:HGNC Symbol;Acc:6971]

Sequence

>retro_pvam_981
TGTATCATTTCAAATCTGGTCAACTCTACCATCTTAATCACATTAGTTTTCAAGAAAAATGTTGTTTAGAACCCCAGTAA
AATCTTCAGTGTGATAACCCTGGACATTGTCAAAGCCAACAGTCTTGTTGCAGAACTGAATAGTTTGGGTCAAGCTCCAG
TCAGTATTCTTGTCATTGGCAGCCATGCTGGGAAGACCATCTCCCTGATATCTCAGAGCACTCCTAAGGTGGAGTTTCCC
TGAGACCAGTTGTCAACCCTCACCTGGTGAATCTAGGAGGCTGGCATGGCGGTGGTCAAGGCTAAAGCTGGAACAGGCTC
TGCCACCCTGTCTATGGCATATGCCGGAACCAGGTTTGTCTTTTCTCTTGTGGATGCAATAAGTGGAAAAGAAGAAGTCG
TTGAATGTTTACTTGTTATGTCTCAAGAAACAGACTGTCTCAATTTCTCTAAACCATTGCTTCTGAGGAAAAAGAACATC
GAGAAGAATCTAGGCATTGGCAAAATCTCTTTCAAAAAGAAGATGATACCTGACTCCATTCCTGAGCTGAATGGCTTGAT
CAAAAAAAGAGAAGAGCTTGTGAAGAACATAAAA

Alignment

ORF - retro_pvam_981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.15 %
• Parental protein coverage: 59.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CVIANPVNSTIPITSEVFKKHGVYNPSKIFGVTTLDVVRANTFVAELKGLDPARVNVPVIGGHAGKTIIP
          C.I.N.VNSTI.IT..VFKK..V.NPSKIF.V.TLD.V.AN..VAEL..L..A.V...VIG.HAGKTI..
Retrocopy CIISNLVNSTILITL-VFKKNVV*NPSKIFSVITLDIVKANSLVAELNSLGQAPVSILVIGSHAGKTI-S

Parental  LISQCTPKVDFPQDQLTALTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAINGKEGVVECSF
          LISQ.TPKV.FP.DQL..LT..I.EAG..VVKAKAG.GSATLSMAYAG.RFVFSLVDAI.GKE.VVEC..
Retrocopy LISQSTPKVEFP*DQLSTLTW*I*EAGMAVVKAKAGTGSATLSMAYAGTRFVFSLVDAISGKEEVVECLL

Parental  VKSQETDCPYFSTPLLLGKKGIEKNLGIGKLSPFEEKMIADAIPELKASIKKGEEFVKNMK
          V.SQETDC..FS.PLLL.KK.IEKNLGIGK.S.F..KMI.D.IPEL...IKK.EE.VKN.K
Retrocopy VMSQETDCLNFSKPLLLRKKNIEKNLGIGKIS-FKKKMIPDSIPELNGLIKKREELVKNIK

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_981 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010846	1 retrocopy	retro_amel_361,
Canis familiaris	ENSCAFG00000013515	2 retrocopies	retro_cfam_182, retro_cfam_41,
Myotis lucifugus	ENSMLUG00000017795	1 retrocopy	retro_mluc_1948,
Monodelphis domestica	ENSMODG00000013680	1 retrocopy	retro_mdom_1711,
Mustela putorius furo	ENSMPUG00000016000	2 retrocopies	retro_mputfur_1607, retro_mputfur_478,
Mus musculus	ENSMUSG00000019179	1 retrocopy	retro_mmus_2451,
Otolemur garnettii	ENSOGAG00000009705	1 retrocopy	retro_ogar_3068,
Pteropus vampyrus	ENSPVAG00000003397	1 retrocopy	retro_pvam_981 ,
Tupaia belangeri	ENSTBEG00000003190	1 retrocopy	retro_tbel_440,
Tursiops truncatus	ENSTTRG00000014834	1 retrocopy	retro_ttru_1550,
Drosophila melanogaster	FBgn0262559	2 retrocopies	retro_dmel_54, retro_dmel_76,