RetrogeneDB ID: retro_pvam_1094

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_28403:189..1009(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP4
• Ensembl ID: ENSPVAG00000010981
• Aliases: None
• Description: retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]

Sequence

>retro_pvam_1094
TTAGCTGACAAGGAAGTAGTCTTTTATGACTCAGTGGAAGAAATTGTGATGAATGAAGAATAAAAAATATGGTAAAAGAA
CATCCCTTTTTTTAAAAATTTGGTGATAACCCATGATCTGGGGTGGCCCAGCCTAACTGTACAGTGGCTTCCAGAAGTAA
CCTGACCAGAAAGGAAATATTTCTTCATTAATAGACTTATTCTGGGGACACACACACTGGATGAACAAAACCGTTTCATG
ATAGCCAGTGTGTAGCTCCCTAACAATTATGCGCAGTTTAATGCTTCACACATGACAGTGAGAAAGGAGAATTTGGAGGT
TTTGGCTTGGTAGTGGAAAGACTGAAATAGAAATCAAGACCAACCATGAAGGAAAAGCAAACAGGGCACGTTATATGCCC
CAGAACCCTTGTATTATTGTAGCAGAAAACATCCAGTAATATTCTTGTTTTTGACTATACAAAACATCCTCCTACACTGT
ATCTTTCTGGAGAGTTCAACCCAGGCTTGCATCTCCATGGACATCATTAGGAAGGCTATGGGCTTTCTTGGAAGAAAATC
TCAGTATGCACTTACTTAGTGCTTCAGATGACCACACCATCTGTCTATGGGACATCGGTGCTGTTCCAAAAGAGGGAAAA
GCTGTGAATTTGAAGACCATCTTTACAGGGCATAGAGCAGTAGTAGACATTTCCTGGTCATCTGTTCCATGAGTCTCTGT
TTGGGTCAGTTACTGATGATCAGAGACTTAAGATCTGGGATACTCATTCAAACATACTTTCAAACCAAGCCACTCAGTTG
ATGCTCACACTGCTGAAGTC

Alignment

ORF - retro_pvam_1094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.7 %
• Parental protein coverage: 64.94 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGT
          .ADKE..F.D.VEE.V.NEE.KIW.KN.PF...LV.TH.L.WPSLT.QWLP.VT.PE.K.F.I.RL.LGT
Retrocopy LADKEVVFYDSVEEIVMNEE*KIW*KNIPFFKNLVITHDLGWPSLTVQWLPEVT*PERKYFFINRLILGT

Parental  HTSDEQNHLVIASVQLPNDDAQFDASH-YDSEKGEFGGFGSV-SGKIEIEIKINHEGEVNRARYMPQNPC
          HT.DEQN...IASV.LPN..AQF.ASH..DSEKGEFGGFG.V.SGK.EIEIK.NHEG..NRARYMPQNPC
Retrocopy HTLDEQNRFMIASV*LPNNYAQFNASH<HDSEKGEFGGFGLV<SGKTEIEIKTNHEGKANRARYMPQNPC

Parental  IIAT-KTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSW-NPNLSGHLLSASDDHTICLWD
          II...KT.SS..LVFDYTKHP.....SGE.NP.L.L.GH..EGYGLSW...NLS.HLLSASDDHTICLWD
Retrocopy IIVA>KT-SSNILVFDYTKHPPTLYLSGEFNPGLHLHGHH*EGYGLSW<EENLSMHLLSASDDHTICLWD

Parental  ISAVPKEGKVVDAKTIFTGHTAVVEDVSW-HLLHESLFGSVADDQKLMIWDTRSN-NTSKPSHSVDAHTA
          I.AVPKEGK.V..KTIFTGH.AVV.D.SW.HL.HESLFGSV.DDQ.L.IWDT.SN..T.KPSHSVDAHTA
Retrocopy IGAVPKEGKAVNLKTIFTGHRAVV-DISW>HLFHESLFGSVTDDQRLKIWDTHSN<HTFKPSHSVDAHTA

Parental  EV
          EV
Retrocopy EV

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_1094 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 21 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005904	2 retrocopies	retro_btau_1610, retro_btau_630,
Canis familiaris	ENSCAFG00000010527	1 retrocopy	retro_cfam_1550,
Choloepus hoffmanni	ENSCHOG00000004066	6 retrocopies	retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus	ENSCJAG00000001021	7 retrocopies	retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus	ENSCPOG00000015352	3 retrocopies	retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus	ENSECAG00000022784	1 retrocopy	retro_ecab_767,
Echinops telfairi	ENSETEG00000020008	4 retrocopies	retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus	ENSFCAG00000027017	1 retrocopy	retro_fcat_1507,
Homo sapiens	ENSG00000162521	6 retrocopies	retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Macropus eugenii	ENSMEUG00000014379	1 retrocopy	retro_meug_1032,
Myotis lucifugus	ENSMLUG00000000749	2 retrocopies	retro_mluc_2275, retro_mluc_892,
Macaca mulatta	ENSMMUG00000009940	1 retrocopy	retro_mmul_75,
Mustela putorius furo	ENSMPUG00000015214	1 retrocopy	retro_mputfur_104,
Mus musculus	ENSMUSG00000057236	1 retrocopy	retro_mmus_356,
Nomascus leucogenys	ENSNLEG00000002805	6 retrocopies	retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Pongo abelii	ENSPPYG00000001588	6 retrocopies	retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus	ENSPVAG00000010981	2 retrocopies	retro_pvam_1094 , retro_pvam_902,
Rattus norvegicus	ENSRNOG00000021492	1 retrocopy	retro_rnor_1270,
Sarcophilus harrisii	ENSSHAG00000010923	1 retrocopy	retro_shar_399,
Ictidomys tridecemlineatus	ENSSTOG00000012011	1 retrocopy	retro_itri_1168,