RetrogeneDB ID: retro_pvam_134

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1557:57683..58141(-)
• Located in intron of: ENSPVAG00000012538

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKI67IP
• Ensembl ID: ENSPVAG00000016707
• Aliases: None
• Description: MKI67 (FHA domain) interacting nucleolar phosphoprotein [Source:HGNC Symbol;Acc:17838]

Sequence

>retro_pvam_134
TTTTTAGAGTGGCATATTCCATTTAAGAAGCCATCATATCTAGGAGTGAAATGATATAATCAGACCTGGACAATTCAAAA
GCTACAGATGGAGGAGTGATTTAAAAAGAAAGAAAAATTACTCGGGAAGAGATTAGCTAAGAAAGGAATTGATTATAACT
TTCCTTCACTGATTTTATATAAAAAGGGGAAAAAATACTTTGAACACTGATCCTCAAAACTCTACAAATAGCCAGGCTTT
ACCTAAGAAGAAAAAAGGTTTCAGTCAGTCCTAACACTCCTGAAAAGACTGGACAGCCAGGGCCCCATACCAGTTTGTAC
AGCAACATTTTTGGAGAAACAAAAATCTGAAGTGGCTGAAACGAGTGATAAAGATAATGCAACAGTTTCAAATAGCACTT
ATCTGGCATAAAAGAAACACAAGTGACTCAAACACCAATATATTCAAGGGAAAAAAGA

Alignment

ORF - retro_pvam_134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.2 %
• Parental protein coverage: 54.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FREWHIPFKKPSYPAVKRYNQNRTILQKLRMEERFKKKEKLLRKKLAKKGIDYDFPSLILH-KKEKNNAS
          F.EWHIPFKKPSY..VK.YNQ..TI.QKL.MEE.FKKKEKLL.K.LAKKGIDY.FPSLIL..K..KN...
Retrocopy FLEWHIPFKKPSYLGVK*YNQTWTI-QKLQMEE*FKKKEKLLGKRLAKKGIDYNFPSLILY>KRGKNTL-

Parental  NSDPRKSRNSQVLPK-KKKKEVSVTPDTPEKTVDSQGPTPVCTPTFLEKRKSEAAEMNDDDKDNEIV-FK
          N.DP..S.NSQ.LPK...K...SV...T..K..DSQGP.PVCT.TFLEK.KSE.AE....DKDN..V.FK
Retrocopy NTDPQNSTNSQALPK<EEKRFQSVL--TLLKRLDSQGPIPVCTATFLEKQKSEVAETS--DKDNATV<FK

Parental  QPSSGIKETQETELPKRSRKRR
          ...SGIKETQ.T..P..SR..R
Retrocopy *HLSGIKETQVTQTPIYSREKR

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_134 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.

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019387	1 retrocopy	retro_btau_1516,
Choloepus hoffmanni	ENSCHOG00000002227	5 retrocopies	retro_chof_1061, retro_chof_1449, retro_chof_1735, retro_chof_236, retro_chof_2480,
Callithrix jacchus	ENSCJAG00000013386	1 retrocopy	retro_cjac_3076,
Dasypus novemcinctus	ENSDNOG00000005017	2 retrocopies	retro_dnov_1869, retro_dnov_2487,
Erinaceus europaeus	ENSEEUG00000008535	3 retrocopies	retro_eeur_530, retro_eeur_550, retro_eeur_91,
Homo sapiens	ENSG00000155438	5 retrocopies	retro_hsap_1077, retro_hsap_1596, retro_hsap_1609, retro_hsap_1611, retro_hsap_553,
Gorilla gorilla	ENSGGOG00000023498	4 retrocopies	retro_ggor_1213, retro_ggor_1923, retro_ggor_2225, retro_ggor_850,
Loxodonta africana	ENSLAFG00000030731	1 retrocopy	retro_lafr_500,
Microcebus murinus	ENSMICG00000015787	1 retrocopy	retro_mmur_990,
Myotis lucifugus	ENSMLUG00000006481	2 retrocopies	retro_mluc_1217, retro_mluc_1369,
Macaca mulatta	ENSMMUG00000020928	11 retrocopies	retro_mmul_1444, retro_mmul_1544, retro_mmul_2149, retro_mmul_2151, retro_mmul_2225, retro_mmul_2226, retro_mmul_2389, retro_mmul_690, retro_mmul_696, retro_mmul_697, retro_mmul_752,
Monodelphis domestica	ENSMODG00000000152	2 retrocopies	retro_mdom_1271, retro_mdom_737,
Nomascus leucogenys	ENSNLEG00000001163	4 retrocopies	retro_nleu_1756, retro_nleu_1942, retro_nleu_2022, retro_nleu_669,
Pongo abelii	ENSPPYG00000025875	2 retrocopies	retro_pabe_2248, retro_pabe_510,
Pan troglodytes	ENSPTRG00000012419	5 retrocopies	retro_ptro_1072, retro_ptro_1077, retro_ptro_1080, retro_ptro_1378, retro_ptro_415,
Pteropus vampyrus	ENSPVAG00000016707	1 retrocopy	retro_pvam_134 ,
Sorex araneus	ENSSARG00000006252	1 retrocopy	retro_sara_362,
Tupaia belangeri	ENSTBEG00000001123	4 retrocopies	retro_tbel_1731, retro_tbel_3479, retro_tbel_4589, retro_tbel_926,
Vicugna pacos	ENSVPAG00000005847	2 retrocopies	retro_vpac_136, retro_vpac_265,