RetrogeneDB ID: retro_pvam_1237

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_4665:28868..29407(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA4
• Ensembl ID: ENSPVAG00000010677
• Aliases: None
• Description: developmental pluripotency associated 4 [Source:HGNC Symbol;Acc:19200]

Sequence

>retro_pvam_1237
AAAGAGGAACAGCAGGCTGCTGGTGAACCAAGTACACAAAGAACCTCAGGGAAGGGTACCAAACAAAAAAGATCTGTGAA
AGATAACAAAGCTTCTTGTCCACAAAAGATGGTACAAAACCATAAAAGAGAAACATTTCGGAAGAAGATACCTATTCCTC
AATTACCCTCTAAATGACCACCTGTCAACCTGCTTCATGGAGACATCATGAGGGCCTGGTGCCAACAATTAAAACTGGGC
ACCAAAGGCTTGAAACTGGAAGCATATAAGAGACTCTGTGGATATGCTTACCCTAATTAAAAGGACATTCTTGTCACAGC
AAAGGAGGCCAAGATCCTGACAAAATCACAAAGAAAATCAAATATGGAAAAGGGGGAATTGACTCTGGAAAGTTCTGATC
CTTCTGAAGTCACTGCTCCCCCTGAGGAAGGGGTGCCCTCTCTTGAAAGGTCTACTGCTCTCCTTGAGGGAATGGACGTT
GTTGTCATGACAGCTTCCATGCGGATGCTATGTTTGCTTCCTGGATCAGAACTGCAGCC

Alignment

ORF - retro_pvam_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.51 %
• Parental protein coverage: 60.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEEQRAAGEPSMQKTSGKGTKRKRPIEADKASCPQKMAQDDKKVKLRKKIPIPPLPSKLPPVNLLHRDIV
          .EEQ.AAGEPS.Q.TSGKGTK.KR.....KASCPQKM.Q..K....RKKIPIP.LPSK.PPVNLLH.DI.
Retrocopy KEEQQAAGEPSTQRTSGKGTKQKRSVKDNKASCPQKMVQNHKRETFRKKIPIPQLPSK*PPVNLLHGDIM

Parental  RAWCQQLKLCTKGLKLDVYRRLCEYAYPNQKDIPITAKEAKILTKSQIKLKMKRGEITL---DPSEMTAV
          RAWCQQLKL.TKGLKL..Y.RLC.YAYPN.KDI..TAKEAKILTKSQ.K..M..GE.TL...DPSE.TA.
Retrocopy RAWCQQLKLGTKGLKLEAYKRLCGYAYPN*KDILVTAKEAKILTKSQRKSNMEKGELTLESSDPSEVTAP

Parental  FKEGASVLEGSTALLDEMDNVVMTTST-PNAVFASWTRIAA
          ..EG...LE.STALL..MD.VVMT.S....A.FASW.R.AA
Retrocopy PEEGVPSLERSTALLEGMDVVVMTASM<ADAMFASWIRTAA

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_1237 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 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010335	5 retrocopies	retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus	ENSCJAG00000020171	2 retrocopies	retro_cjac_1334, retro_cjac_1491,
Echinops telfairi	ENSETEG00000002722	1 retrocopy	retro_etel_312,
Homo sapiens	ENSG00000121570	1 retrocopy	retro_hsap_893,
Gorilla gorilla	ENSGGOG00000015121	2 retrocopies	retro_ggor_1970, retro_ggor_723,
Loxodonta africana	ENSLAFG00000016804	1 retrocopy	retro_lafr_456,
Myotis lucifugus	ENSMLUG00000016423	1 retrocopy	retro_mluc_973,
Macaca mulatta	ENSMMUG00000016901	1 retrocopy	retro_mmul_1515,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mustela putorius furo	ENSMPUG00000010206	1 retrocopy	retro_mputfur_800,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Nomascus leucogenys	ENSNLEG00000004030	3 retrocopies	retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus	ENSOCUG00000016435	1 retrocopy	retro_ocun_114,
Pongo abelii	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus	ENSPVAG00000010677	1 retrocopy	retro_pvam_1237 ,
Rattus norvegicus	ENSRNOG00000025404	4 retrocopies	retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tursiops truncatus	ENSTTRG00000009508	1 retrocopy	retro_ttru_1772,