RetrogeneDB ID: retro_pvam_487

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_343:151355..151872(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A1
• Ensembl ID: ENSPVAG00000015225
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]

Sequence

>retro_pvam_487
ATGGTTCCAATGAACCACCCAGCCCCTGTGGAAGTCACATACAGGAACATGAGATTTCTTATTGCACACAATCCAACCAG
TGCAACCTTAAACAAATTTATAGAGGAACTTAAGAAATATGACATTACCACAATAGTAAAAGTGTATGAAGCAACTTATG
ATACTGCTCTTGTGGAGAAAGAAGCATCCAGGTTCTGGATTGGCTTTTTAATAATGGTTCATCACCGTCTAACCAGATTG
TTGATGATTGGTTAAATCTGTAAACGTCAAATTTCGTGAAGAACCTGGTTGTTGTATTGCTGTTTACTGTGTTGTAGGTC
TGGGGAGAACTCCAATGCTTGTTGCTCTAGCGGTAATCAAAGGTGGAATGAAAAATGAAGATGTAGTACCGTTTATATGA
CAAAAACGGTGTGGAACTTTTAACAGCAAGCAACTTTTGTATTTGGAGAAATATCGTTCTAAGATGCAGCTGCACTTCAA
AGACACCAGCGGTCATAGAAACAAATGTTGCATTCAA

Alignment

ORF - retro_pvam_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MARMNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEG-IHVLDWP
          M..MN.PAPVEVTY.NMRFLI.HNPT.ATLNKFIEELKKY..TTIV.V.EATYDT.LVEKE..I.VLDW.
Retrocopy MVPMNHPAPVEVTYRNMRFLIAHNPTSATLNKFIEELKKYDITTIVKVYEATYDTALVEKEA<IQVLDWL

Parental  FDDGAPPSNQIVDDWLSL-VKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRR
          F..G..PSNQIVDDWL.L.V..KFREEPGCCIAV.CV.GLGR.P.LVALA.I.GGMK.ED.V.FI.QKR.
Retrocopy FNNGSSPSNQIVDDWLNL<VNVKFREEPGCCIAVYCVVGLGRTPMLVALAVIKGGMKNEDVVPFI*QKRC

Parental  GAFNSKQLLYLEKYRPKMRLRFKDSNGHRNNCCVQ
          G.FNSKQLLYLEKYR.KM.L.FKD..GHRN.CC.Q
Retrocopy GTFNSKQLLYLEKYRSKMQLHFKDTSGHRNKCCIQ

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_487 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 16 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002275	3 retrocopies	retro_btau_1051, retro_btau_1186, retro_btau_859,
Equus caballus	ENSECAG00000022483	6 retrocopies	retro_ecab_10, retro_ecab_1075, retro_ecab_20, retro_ecab_425, retro_ecab_783, retro_ecab_869,
Echinops telfairi	ENSETEG00000008183	6 retrocopies	retro_etel_1485, retro_etel_1681, retro_etel_1698, retro_etel_18, retro_etel_2153, retro_etel_668,
Latimeria chalumnae	ENSLACG00000007183	1 retrocopy	retro_lcha_90,
Loxodonta africana	ENSLAFG00000006572	8 retrocopies	retro_lafr_1054, retro_lafr_1120, retro_lafr_1133, retro_lafr_328, retro_lafr_670, retro_lafr_7, retro_lafr_780, retro_lafr_939,
Myotis lucifugus	ENSMLUG00000001162	1 retrocopy	retro_mluc_264,
Macaca mulatta	ENSMMUG00000002777	1 retrocopy	retro_mmul_1720,
Monodelphis domestica	ENSMODG00000018701	5 retrocopies	retro_mdom_1630, retro_mdom_1864, retro_mdom_363, retro_mdom_729, retro_mdom_927,
Nomascus leucogenys	ENSNLEG00000000440	6 retrocopies	retro_nleu_1111, retro_nleu_1159, retro_nleu_1681, retro_nleu_169, retro_nleu_407, retro_nleu_893,
Oryctolagus cuniculus	ENSOCUG00000006311	4 retrocopies	retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
Pongo abelii	ENSPPYG00000016743	5 retrocopies	retro_pabe_2058, retro_pabe_255, retro_pabe_2660, retro_pabe_3732, retro_pabe_721,
Pteropus vampyrus	ENSPVAG00000015225	2 retrocopies	retro_pvam_487 , retro_pvam_848,
Rattus norvegicus	ENSRNOG00000011771	4 retrocopies	retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus	ENSRNOG00000046370	4 retrocopies	retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
Tupaia belangeri	ENSTBEG00000009956	14 retrocopies	retro_tbel_1216, retro_tbel_1392, retro_tbel_2167, retro_tbel_2236, retro_tbel_23, retro_tbel_2549, retro_tbel_2570, retro_tbel_2611, retro_tbel_3144, retro_tbel_3295, retro_tbel_3424, retro_tbel_4074, retro_tbel_4123, retro_tbel_869,
Tursiops truncatus	ENSTTRG00000004129	6 retrocopies	retro_ttru_34, retro_ttru_450, retro_ttru_571, retro_ttru_642, retro_ttru_643, retro_ttru_69,