RetrogeneDB ID: retro_pabe_3729

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:24442110..24443580(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM48A
• Ensembl ID: ENSPPYG00000005288
• Aliases: SUPT20H, FAM48A
• Description: protein FAM48A [Source:RefSeq peptide;Acc:NP_001128975]

Sequence

>retro_pabe_3729
ATGGATCGAGATTTAGAACAGGCTCTGGATCGCGCAGAGAATATCACTGAAATTGCCCAACAGAGACCTCCTAGGAGGAG
ATACTCACCTAGGGCGGGAAAAACTCTACAGGAAAAACTTTATGACATTTATGTTGAAGAATGTGGAAAAGAGCCTGAGG
ATCCTCAGGAATTGAGAAGCAATGTAAACTTGTTACAAAAGCTTGTTAGGAGAGATTCCTTGCCATGTTTACTGGTCAAT
CTATACCCAGGCAATCAGGGGTATTCTGTGATGCTCCAGAGAGAAGATGGGTCCCTTGCAGAGACCATTCGGCTGCCTTA
CGAAGAAAGGGCATTGCTCGACTACTTGGATGCAGAAGAATTACCCCCTGCTTTGGGTGATGTCCTGGATAAAGCTTCGG
TTAACATTTTTCATAGTGGGTGTGTCATAGTAGAAGTTCGTGACTACAGGCAGTCCAGTAATCTGCAACCTCCTGGTTCC
CAAAGCAGGCATATTCTCCTACGTCCAACGATGCAGACTTTAGCCCATGATGTGAAGATGATGACAAGAGATGGCCAGAA
ATGGAGCCAGGAAGACAAATTTCCGCTTGAGAGTCAACTGATCTTAGAGACAGCTGAACCACTGTGTCTCGATCCTTCTG
TAGCAGTCGCCTGCACTGCAAACAGGCTGCTGTACAACAAGCAAAAGATGAAGACTGACCCGATGAAACAGTGCCTCCAG
AGGTATTCGTGGCCCTCTGTAAAGCCACAGCAGGAGCAGTCTGACTGTCCACCTCCTCCTGAGCTGACAGTGTCGACTTC
TGGCCAAAAAGAAGAAAGAAAAGCAGGTCAGCCTTGTGAGCTGAACATTGCTAAAGCAGGAAGTTGTGTAGACACGTGGA
AACGCAGACCCTGTGATTTGGCCGTGCCTTCAGAAGTGGATGTGGAGAAACTTGCTAAAGGGTATCAGTCCGTCACAGCT
GCTGACCCACAGCTCCCAGTCTGGCCAGCCCAGGAGGTAGAAGACCCTTTCAGATTTGCATGGGAAGCTGGCTGTCAGGC
CTGGGACACCAAGCCAAACATCACGCAGTCGTTTAATGATCCGGTTTTCAGTGGTGAAATATGGCCACATAAAAAAGCCA
GGCAGAAGAGCCAGAAGTCTCCCTGGCAGCCCTTCCCAGATGACCATTCAGCTTGTCCCAGGCCTGGGTCAGAGACTGAT
GCTGGGAGGGCAGTGAGTCAGGCCCAGGAATCAGTGCAGAGCAAAGTCAAAGGTCCAGGCAAGATGTCACACAGCTCCAG
TGGCCCAGCCAGTGTCAGTCAGCTCTCTTCATGGAAAACACCAGAACAGCCTGATCCTGTGTGGGTCCAGTCTTCAGTAT
TGGGGAAGGGAGAGAAACATCCACCTCCCCACACCCAACTTCCCTCAAGCTCGGGAAAGATTTCCTCAGGTAACAGTTTT
CCCCCACAACAGGCAAGCAGCCCTCTTAAG

Alignment

ORF - retro_pabe_3729 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.1 %
• Parental protein coverage: 62.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQALELALDRAEYVIESARQRPPKRKYLSSGRKSVFQKLYDLYIEECEKEPE-VKKLRRNVNLLEKLVM
          M...LE.ALDRAE...E.A.QRPP.R.Y.....K....KLYD.Y.EEC.KEPE....LR.NVNLL.KLV.
Retrocopy MDRDLEQALDRAENITEIAQQRPPRRRYSPRAGKTLQEKLYDIYVEECGKEPEDPQELRSNVNLLQKLVR

Parental  QETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEELPPILVDLLEKSQVNIFHCG
          ...L.CL.VNLYPGN.GYS.ML....GS..ETIRLPYEE..LL.YLDAEELPP.L.D.L.K..VNIFH.G
Retrocopy RDSLPCLLVNLYPGNQGYSVMLQREDGSLAETIRLPYEERALLDYLDAEELPPALGDVLDKASVNIFHSG

Parental  CVIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSITSDNHKWTQEDKLLLESQLILATAEPLCL
          CVI.E.RDYRQSSN...PG.QSRHILLRPTMQTL..DV...T.D..KW.QEDK..LESQLIL.TAEPLCL
Retrocopy CVIVEVRDYRQSSNLQPPGSQSRHILLRPTMQTLAHDVKMMTRDGQKWSQEDKFPLESQLILETAEPLCL

Parental  DPSIAVTCTANRLLYNKQKMNTRPMKRCFKRYSRSSLNRQQDLSHCPPPPQLSYLISYKKKGRKAGQHYD
          DPS.AV.CTANRLLYNKQKM.T.PMK.C..RYS..S...QQ..S.CPPPP.L....S..K..RKAGQ...
Retrocopy DPSVAVACTANRLLYNKQKMKTDPMKQCLQRYSWPSVKPQQEQSDCPPPPELTVSTSGQKEERKAGQPCE

Parental  LK-SKAGNCVDMWKRSPCNLAIPSEVDVEKYAKVEKSIKSDDSQPTVWPAHDVKDDYVFECEASTQYQKT
          L...KAG.CVD.WKR.PC.LA.PSEVDVEK.AK...S....D.Q..VWPA..V.D...F..EA..Q...T
Retrocopy LNIAKAGSCVDTWKRRPCDLAVPSEVDVEKLAKGYQSVTAADPQLPVWPAQEVEDPFRFAWEAGCQAWDT

Parental  KLTILQSLGDPLYYGKIQPCKADEESDSQMSPSHSSTDDHSNWFIIGSKTDAERVVNQYQELVQNEAKCP
          K..I.QS..DP...G.I.P.K......SQ.SP.....DDHS.....GS.TDA.R.V.Q.QE.VQ...K.P
Retrocopy KPNITQSFNDPVFSGEIWPHKKARQK-SQKSPWQPFPDDHSACPRPGSETDAGRAVSQAQESVQSKVKGP

Parental  VKMSHSSSGSASLSQVSPGKETEQTETVSVQSSVLGKGVKHRPPPIKLPSSSGNSSSGNYFTPQQTSSFL
          .KMSHSSSG.AS.SQ.S..K..EQ...V.VQSSVLGKG.KH.PP...LPSSSG..SSGN.F.PQQ.SS.L
Retrocopy GKMSHSSSGPASVSQLSSWKTPEQPDPVWVQSSVLGKGEKHPPPHTQLPSSSGKISSGNSFPPQQASSPL

Parental  K
          K
Retrocopy K

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.42 RPM
SRP007412_cerebellum	0.00 RPM	32.95 RPM
SRP007412_heart	0.00 RPM	8.46 RPM
SRP007412_kidney	0.00 RPM	18.83 RPM
SRP007412_liver	0.00 RPM	13.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3729 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3729 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4794
Pan troglodytes	retro_ptro_3189
Macaca mulatta	retro_mmul_2555
Equus caballus	retro_ecab_1101

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000116	2 retrocopies	retro_ecab_1052, retro_ecab_1101,
Homo sapiens	ENSG00000102710	2 retrocopies	retro_hsap_4659, retro_hsap_4794,
Loxodonta africana	ENSLAFG00000027507	1 retrocopy	retro_lafr_1199,
Macaca mulatta	ENSMMUG00000003590	2 retrocopies	retro_mmul_2479, retro_mmul_2555,
Pongo abelii	ENSPPYG00000005288	2 retrocopies	retro_pabe_3619, retro_pabe_3729 ,
Pan troglodytes	ENSPTRG00000005791	2 retrocopies	retro_ptro_3095, retro_ptro_3189,
Pteropus vampyrus	ENSPVAG00000014609	1 retrocopy	retro_pvam_401,
Tarsius syrichta	ENSTSYG00000013227	1 retrocopy	retro_tsyr_2160,
Vicugna pacos	ENSVPAG00000007288	1 retrocopy	retro_vpac_193,