RetrogeneDB ID: retro_pvam_370

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2773:79565..80621(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMCL1
• Ensembl ID: ENSPVAG00000001242
• Aliases: None
• Description: germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]

Sequence

>retro_pvam_370
CTGCACTTTGTACTAGGCTCGTTGTACTGGGATGAATATGTCTTAAGGGAGCCCCTTCGAGTTCCACGAATTTTGGCAAC
AGCACGCCTGCTTCAAGTAGAGAAGTTAGTTCGGCATTGTGGTGAGACCATGAAGGAAACAATTAATGCAAAAACTGTGT
GTAGCTATTATGCAGCAGCAGAAACCTATGGATTAGAGTCTGTAAAGACAGAGTGCTTCGAATGGCTTCTCCACAATTTG
ATGACACATCCAAGTATTCAACTGTACAAAGAACTCAGCATAGATCTCATGAAAATGCTCATTTCTTCTTCTAATTTATT
AGTAATGCAAAAGGAAATGGATGTGTACACCACACTTAAAGAGTGGATGTTCATTCGTCTTAACCCAGCTTGGAAAGGCT
CAATAAGACAGCTTTTAGTTCATGCAAACCAATGGTTTTCCAGGCACAGGGAAGCTGTGAATGCCATTGCCTTTCTTGAA
ACCACAGAAGGCATAGCATTTCAACCAGTGTTTAAAAAGTTGAGGTTTCACCATATGATCTGCGACCTGGCCTCCACGAG
GGTTATTGAGCAAGATACTGTGATACCTTCTGAATGGTTATCATATGTTTATAAACAACAATGGTTTACCTTGCTTAAAG
CAGAACAAAACAGAGAAATTGGGCCCCGAGACATCAATGAAACAGAGCTTGAAGGATATAGCATGAGATGTGGTAAAAAG
ATTCTCAAAGATGGAAAATACTCCTGGAATTGGTCAGGTTACAACTTTGGCTTTCCATTACATGTTACCTTCAACAGTCA
TTATATAATTTTCAAGCAAAATACTTTCAATCATTCATGTGACAATTCAGTTTGTTTAAAATTTCTAAGAAATATCGTGT
TCAGATTAACTTTGGTATATTTCAATTCTAAGGGAAAACTAAGTTTCAGCAAAACAACCGGTTATAAAATTCTTACTTTT
GAAAAGGATGAAGAACAAGTGATAATGAAGTTGGATAGCATAGTTCTGAGATTCCCTTTATACATATTCTGTAACTTCCT
GTTTATGCCATTAGAA

Alignment

ORF - retro_pvam_370 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.38 %
• Parental protein coverage: 68.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQVAFGSLYRDD-VLIKPSRVIAILAAACMLQLDGLIQQCGETMKETINVKTVCGYYTSAGTYGLDSVKK
          L....GSLY.D..VL..P.RV..ILA.A..LQ...L...CGETMKETIN.KTVC.YY..A.TYGL.SVK.
Retrocopy LHFVLGSLYWDEYVLREPLRVPRILATARLLQVEKLVRHCGETMKETINAKTVCSYYAAAETYGLESVKT

Parental  KCLEWLLNNLMTHQNVELFKELSINVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSLKQLLT
          .C.EWLL.NLMTH....L.KELSI..MK.LI.SSNL.VMQ.EMDVYT.LK.WMF..L.P.W.GS..QLL.
Retrocopy ECFEWLLHNLMTHPSIQLYKELSIDLMKMLISSSNLLVMQKEMDVYTTLKEWMFIRLNPAWKGSIRQLLV

Parental  ETDVWFSKRRKDFEGMTFLETEQGKPFASVFRQLRLQYIISDLASARIIEQDSLVPSEWLSSVYKQQWLA
          ....WFS..R.......FLET..G..F..VF..LR....I.DLAS.R.IEQD...PSEWLS.VYKQQW..
Retrocopy HANQWFSRHREAVNAIAFLETTEGIAFQPVFKKLRFHHMICDLASTRVIEQDTVIPSEWLSYVYKQQWFT

Parental  MLRAEQDSEVGPQEINKEELEGNSMRCGRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNTLNQPC
          .L.AEQ..E.GP..IN..ELEG.SMRCG.K..KDG.Y.W.W.G.NFGF.L.VT....YIIFK.NT.N..C
Retrocopy LLKAEQNREIGPRDINETELEGYSMRCGKKILKDGKYSWNWSGYNFGFPLHVTFNSHYIIFKQNTFNHSC

Parental  SGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMNLDSRLLIFPLYICCNFLYIS
          ..SV.L...R.I.FRL.L..F.S.GKL..S.TTGY.ILT.EKD.EQV.M.LDS..L.FPLYI.CNFL...
Retrocopy DNSVCLKFLRNIVFRLTLVYFNSKGKLSFSKTTGYKILTFEKDEEQVIMKLDSIVLRFPLYIFCNFLFMP

Parental  PE
          .E
Retrocopy LE

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_370 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562, retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109, retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370 , retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,