RetrogeneDB ID: retro_pvam_912

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_16224:19594..20646(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLG2
• Ensembl ID: ENSPVAG00000004554
• Aliases: None
• Description: succinate-CoA ligase, GDP-forming, beta subunit [Source:HGNC Symbol;Acc:11450]

Sequence

>retro_pvam_912
ATTGTTTTAAAAGCCCAGAAATTAGCTGGAGGAAGAGGAAAGGTAACTTCAGTAGCAGTTTGAAAGGAGACATTCATTTA
ACAAATACTCTAAAGTTGTAGGAAAGCTGGCTGAACAGATGATTAGGTATAACGTAGCAATAAAACAATTTCCAAAAGAA
CTAGAAGTTAATAAGGTGATGGTTGCTGAAGCCTTGGACATTTCCAGAGAAACCTACTTTGCGATTCTGATAGACTGGTC
CTGCAATGGCCCTGTCCTGATGGGCAGCCTCCAAAGGGGCGTTGACATTGAAGTGGTGGCAGCTTCAAACTCAGACCTTA
TTTTTAAAGAGCAAATTGACATTATTGAAGGGATAAAGGACAGTCAAGTTCAGCAGGTGGCAGAAATTCTAGTTTTTTGG
GGGGCCTTTGAAAAACCAGGCTGCAGATCAAGTTAAGAAGCTGTATTATCTCTTCCTGAAACTGATGCTACTCAGGTGGA
AGTGAACCCCTTTGGTGAAACTCCAGAAGGAACAAGTTTACCTCTGATGCCAAGATAAACTTTGATGACAACACAGAACT
TTGACAAAAGGACATATTTGCTTTGACTGACAAGTCAGAGAATGAGCCCATTGAAAATGAAACTGCCAGATATGAGACTA
AATAAATAGGGCTGGATGAGAACACTGCCTGCATTGTGAATTGGGCTGGACTCGCCATTGAGGCTTGTGATATAATTTTC
CTGAATGGTGAGAAACCAGCCAACTTCTTGGATCATGGTAATGGTGTAAAGGAAGCTCAAGTATATCAAGACTTTAAATT
GTTCACAGTTGAATCAATGGTTGAAGTAATCATTATTAATATTTTTGGTGGAATTATCAACTGTACCATCATTGTCAATG
AAATCACCAAAGCCTGCTGAGAGCTCAAACTTAAGGTGCCCCTGGTGATCTGGCTTGAGGGAACCAATGTCCACGAGGCC
CAGAAGATACTCAGTAATAGTGGGCTCCAAATACTTTGGCCATTGACCTGGAAGATGCAACCAATAAGGCTGTGGCCAGA
GTGGCTAAGAAG

Alignment

ORF - retro_pvam_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 81.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  IVLKAQILAGGRGK-GIFSSGLKGGVHLT-KDPKVVGKLAKQMIGYNLATKQTPKEGVKVNKVMVAEALD
          IVLKAQ.LAGGRGK.G.FSS.LKG..HLT.K..KVVGKLA.QMI.YN.A.KQ.PKE...VNKVMVAEALD
Retrocopy IVLKAQKLAGGRGK<GNFSSSLKGDIHLT<KYSKVVGKLAEQMIRYNVAIKQFPKE-LEVNKVMVAEALD

Parental  ISRETYFAILMDRSYNGPVLVGSPQGGIDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFLG-P
          ISRETYFAIL.D.S.NGPVL.GS.Q.G.DIE.VAASN..LIFKEQIDIIEGIKDSQ.Q..AE.L.F.G.P
Retrocopy ISRETYFAILIDWSCNGPVLMGSLQRGVDIEVVAASNSDLIFKEQIDIIEGIKDSQVQQVAEILVFWG>P

Parental  LKNQAADQIKKLYNLFLKI-DATQVEVNPFGETPEGQVVCF-DAKINFDDNAEFRQKDIFAMDDKSENEP
          LKNQAADQ.KKLY.LFLK..DATQVEVNPFGETPEG......DAKINFDDN.E..QKDIFA..DKSENEP
Retrocopy LKNQAADQVKKLYYLFLKL<DATQVEVNPFGETPEGTSLPL<DAKINFDDNTEL*QKDIFALTDKSENEP

Parental  ---EAARYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKEAQVYQAFKLLTADPK
          ...E.ARY..K.IGLD.N.AC.VN.AGLA...CDIIFLNG.KPANFLD.G.GVKEAQVYQ.FKL.T....
Retrocopy IENETARYETK*IGLDENTACIVNWAGLAIEACDIIFLNGEKPANFLDHGNGVKEAQVYQDFKLFTVESM

Parental  VEAILVNIFGGIVNCAIIANGITKACRELELKVPLVIRLEGTNVHEAQKILSNSGL-PITSAIDLEDAAK
          VE.I..NIFGGI.NC.II.N.ITKAC.EL.LKVPLVI.LEGTNVHEAQKILSNSGL.P.T.AIDLEDA..
Retrocopy VEVIIINIFGGIINCTIIVNEITKAC*ELKLKVPLVIWLEGTNVHEAQKILSNSGL<PNTLAIDLEDATN

Parental  KAVASVAKK
          KAVA.VAKK
Retrocopy KAVARVAKK

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_912 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000172340	1 retrocopy	retro_hsap_1044,
Gorilla gorilla	ENSGGOG00000027438	1 retrocopy	retro_ggor_825,
Myotis lucifugus	ENSMLUG00000017294	1 retrocopy	retro_mluc_695,
Macaca mulatta	ENSMMUG00000009693	2 retrocopies	retro_mmul_1273, retro_mmul_1995,
Mus musculus	ENSMUSG00000061838	1 retrocopy	retro_mmus_3720,
Nomascus leucogenys	ENSNLEG00000007553	1 retrocopy	retro_nleu_915,
Otolemur garnettii	ENSOGAG00000006190	1 retrocopy	retro_ogar_161,
Pongo abelii	ENSPPYG00000013735	1 retrocopy	retro_pabe_2624,
Pteropus vampyrus	ENSPVAG00000004554	1 retrocopy	retro_pvam_912 ,