RetrogeneDB ID: retro_pvam_1027

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_23385:1619..2124(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSPVAG00000017902
• Aliases: None
• Description: cyclin G1 [Source:HGNC Symbol;Acc:1592]

Sequence

>retro_pvam_1027
ATAAGCCAGTATAGGTTCACAGTTTCAGAGTGGATGAGATTGGAAAAGATTGTGTTGGACGAGGTGTGTTGTAAAGTCAA
AGCTACTACTACCTTTCAATTTCTGCAACTCTATTATTTGCCCATTCAAGAGAACTTGCCATTTGAAAGGAGTAATAACC
TTAATTTTGAAAGAGCTTCTTGCTCAACCTAAGGCATACCAATGCAGGATTATATTTTCTAAAACAAAGCCTTTCGTGTT
CTCATTGTCTATTATTCCCTTGGAGATCTAAGCACAGAAACATGTAGAATTAACAAAAGGAGTAACATGTCTTAAAAAAC
ATCCCAAATTAAATGGCAGAGTTTTGATCTTCTGACAAGAGTTTGTATCCAAGTGTTTAACTGAATATTCATCAAACAAG
TGTTCCAAACCAAATGTACAGAATTGTTTCTGGGTGTATTGCATGGCAATTTAAGTATAGTTACTAAGAATAATCTACCT
TTTAACAGTTCCAGAAACAGTCCCT

Alignment

ORF - retro_pvam_1027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.05 %
• Parental protein coverage: 56.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISQYRFTVSDLMRMEKIVLEKVCWKVKATTAFQFLQLYYSLIQENLPFERRNSLNFER-LEAQLKACHCR
          ISQYRFTVS..MR.EKIVL..VC.KVKATT.FQFLQLYY..IQENLPFER.N.LNFER.L.AQ.KA..CR
Retrocopy ISQYRFTVSEWMRLEKIVLDEVCCKVKATTTFQFLQLYYLPIQENLPFERSNNLNFER>LLAQPKAYQCR

Parental  IIFSKAKPSVLALSIIALEIQAQKCVELTEGVGCLQKHSKINGRDLTFWQELVSKCLTEYSSNKCSKPNV
          IIFSK.KP.V..LSII.LEI.AQK.VELT.GV.CL.KH.K.NGR.L.F.QE.VSKCLTEYSSNKCSKPNV
Retrocopy IIFSKTKPFVFSLSIIPLEI*AQKHVELTKGVTCLKKHPKLNGRVLIF*QEFVSKCLTEYSSNKCSKPNV

Parental  QKLKWIVSGRTARQLKHSYYRITHLPTIP
          Q...W.........L....Y..T...T.P
Retrocopy QNCFWVYCMAI*V*LLRIIYLLTVPETVP

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_1027 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006607	2 retrocopies	retro_btau_1064, retro_btau_763,
Canis familiaris	ENSCAFG00000017207	1 retrocopy	retro_cfam_1657,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Dipodomys ordii	ENSDORG00000014293	1 retrocopy	retro_dord_486,
Equus caballus	ENSECAG00000018880	1 retrocopy	retro_ecab_152,
Felis catus	ENSFCAG00000027366	1 retrocopy	retro_fcat_763,
Myotis lucifugus	ENSMLUG00000001667	1 retrocopy	retro_mluc_1341,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
Pteropus vampyrus	ENSPVAG00000017902	1 retrocopy	retro_pvam_1027 ,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,