RetrogeneDB ID: retro_pvam_75

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1242:168312..168691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPRKB
• Ensembl ID: ENSPVAG00000012419
• Aliases: None
• Description: TP53RK binding protein [Source:HGNC Symbol;Acc:24259]

Sequence

>retro_pvam_75
ATGCAGTTAGCATATCAGCTAGACCTATTTTTCTAATGCAGGGTGACCCTTCTGTTATTTAAAGATGTAAAACAATGTTG
AAGACTTGAAAAAAAAGGCCATGGAAGGTGCCATTGATGGATAATTAATAAAATCTACAGGGACTGTCGATCTATTTCAG
ATGCTTATGGCAGAAAACAAAGTGATTTACCTCCACAAACTGGGGAAAATTGAAGACATTAACTTTACCTGCTGAAATGA
TTTTCAGCCTTTCCCCAAATAATATTTCAGAAGCTATGAAAAACTTGATATCTCAGCAAGTGACACTTTAATTCTAATTG
TTTATGTCGAAGATAGAGAAAAACAAAATCATGACCTAATATTTCAGGTAGAAGGTTAT

Alignment

ORF - retro_pvam_75 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 73.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQLTQQLDLFPECKVTLLLFKDVK-NAGVLRKKAMEGAIVGSLINPTMIIDPFQVVVAANKAVHLYKL-G
          MQL..QLDLF..C.VTLLLFKDVK.N...L...AMEGAI.G.LI..T...D.FQ...A.NK...L.KL.G
Retrocopy MQLAYQLDLFF*CRVTLLLFKDVK>NVEDLXXXAMEGAIDG*LIKSTGTVDLFQMLMAENKVIYLHKL>G

Parental  KMKTRTLYTEVIFNLSPNNHISEALKT-FGTSANDTSILIVYIEDGEKQVDQEDLLSQIEGH
          K.KT.TL..E.IF.LSPNN.ISEA.K.....SA.DT.ILIVY.ED.EKQ....DL..Q.EG.
Retrocopy KLKTLTLPAEMIFSLSPNN-ISEAMKN<LDISASDTLILIVYVEDREKQ--NHDLIFQVEGY

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_75 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 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012021	1 retrocopy	retro_chof_35,
Callithrix jacchus	ENSCJAG00000004162	3 retrocopies	retro_cjac_1999, retro_cjac_2867, retro_cjac_3065,
Homo sapiens	ENSG00000144034	1 retrocopy	retro_hsap_552,
Gorilla gorilla	ENSGGOG00000009062	1 retrocopy	retro_ggor_501,
Macaca mulatta	ENSMMUG00000030805	1 retrocopy	retro_mmul_1571,
Monodelphis domestica	ENSMODG00000016950	2 retrocopies	retro_mdom_1264, retro_mdom_465,
Nomascus leucogenys	ENSNLEG00000000300	2 retrocopies	retro_nleu_2021, retro_nleu_957,
Oryctolagus cuniculus	ENSOCUG00000016251	2 retrocopies	retro_ocun_519, retro_ocun_769,
Otolemur garnettii	ENSOGAG00000032893	2 retrocopies	retro_ogar_523, retro_ogar_849,
Pongo abelii	ENSPPYG00000012292	1 retrocopy	retro_pabe_509,
Pteropus vampyrus	ENSPVAG00000012419	1 retrocopy	retro_pvam_75 ,
Ictidomys tridecemlineatus	ENSSTOG00000016406	4 retrocopies	retro_itri_1613, retro_itri_453, retro_itri_918, retro_itri_919,
Tupaia belangeri	ENSTBEG00000014584	2 retrocopies	retro_tbel_33, retro_tbel_3630,
Vicugna pacos	ENSVPAG00000007934	2 retrocopies	retro_vpac_149, retro_vpac_192,