RetrogeneDB ID: retro_pvam_690

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_728:204416..205014(+)
• Located in intron of: ENSPVAG00000009125

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS6
• Ensembl ID: ENSPVAG00000005186
• Aliases: None
• Description: COP9 signalosome subunit 6 [Source:HGNC Symbol;Acc:21749]

Sequence

>retro_pvam_690
GAGGGCAGAAATATCAAGGTGATAAACTCTTCTGAGCTACTGTCACACAACATGGAGGAGAAAATTATCATTGACAAGGA
ATATTATTAAACCGAGGAGGAGCAATTTAAACACATATTCCAGGAGCTGCGGTTTGGGCGTTGTTATTTCACAGAGATGC
AGCCTGACCCTTGTGGCTTACTTGTCTATAAGAAGGTGTGTGAGATAATCAAGAGCTCCCTCTCTCTCTTTCTTAAGTTG
AACCCTATGACCAAGCACACAGATCTTCCCATCAGCATTTTTGAGTCCGTCATCAATGTAATCAGTGGAGCGGCCACAGT
GCTGTTTGCTGAGCTGACCTACACTCTGGCTACAGAGGAAGCTGAAGGTACTGGTGTGGAACATGTGGCCCCAATGACAG
CAACAAGCAATGGAGAGAACTCCACTGTGGCTGAACACCTGATAGCACAGCACAGTACCATCAGGATACTGCACAGCCTG
TGTCATGCTCATCTCGGAGTATGTCAAAGCCCCTGAAGCAGGAGAGGTCCCCTTTAACTGTGAGATCCTGCGGGAGGCCT
ATGCTCTGTGTCACGGTCTCCCAGTACTCAATACGGAC

Alignment

ORF - retro_pvam_690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74. %
• Parental protein coverage: 60.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGRNIEVMNSFELLSHTVEEKIIIDKEYYYTKEEQFKQVFKELEFLGWYTTGGPPDPSDIHVHKQVCEII
          EGRNI.V.NS.ELLSH..EEKIIIDKEYY.T.EEQFK..F.EL.F...Y.T...PDP....V.K.VCEII
Retrocopy EGRNIKVINSSELLSHNMEEKIIIDKEYY*TEEEQFKHIFQELRFGRCYFTEMQPDPCGLLVYKKVCEII

Parental  ESP--LFLKLNPMTKHTDLPVSVFESVIDIINGEATMLFAELTYTLATEEAERIGVDHVARMTATGSGEN
          .S...LFLKLNPMTKHTDLP.S.FESVI..I.G.AT.LFAELTYTLATEEAE..GV.HVA.MTAT..GEN
Retrocopy KSSLSLFLKLNPMTKHTDLPISIFESVINVISGAATVLFAELTYTLATEEAEGTGVEHVAPMTATSNGEN

Parental  STVAEHLIAQHSAIKMLHSR-VKLILEYVKASEAGEVPFNHEILREAYALCHCLPVLSTD
          STVAEHLIAQHS.I..LHS..V.LI.EYVKA.EAGEVPFN.EILREAYALCH.LPVL.TD
Retrocopy STVAEHLIAQHSTIRILHSL>VMLISEYVKAPEAGEVPFNCEILREAYALCHGLPVLNTD

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_690 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014814	1 retrocopy	retro_cfam_1389,
Felis catus	ENSFCAG00000003561	1 retrocopy	retro_fcat_522,
Macaca mulatta	ENSMMUG00000013440	1 retrocopy	retro_mmul_387,
Monodelphis domestica	ENSMODG00000004170	1 retrocopy	retro_mdom_220,
Otolemur garnettii	ENSOGAG00000016843	1 retrocopy	retro_ogar_1236,
Pteropus vampyrus	ENSPVAG00000005186	1 retrocopy	retro_pvam_690 ,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371,