RetrogeneDB ID: retro_pabe_2906

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:124153268..124154400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSPPYG00000009832
• Aliases: LSM14A, FAM61A
• Description: Protein LSM14 homolog A [Source:UniProtKB/Swiss-Prot;Acc:Q5R4R4]

Sequence

>retro_pabe_2906
TGTGAGCCACCAAAACCACAGTGTTCTTTGCCTGAAGACCCAGCTATCCTTCAGTCCTCACTAGGCTCATCAACTTCTTC
ATTCCGGTGCGTGGGGTTCTCATGGGCCTTTGGGCAGGATGATCATATACAGTCGGTTCAGTCTAAGCTCCTTAGTTGGG
CAGGAGTTTGGTGCCGTTGCTGTTGCTGGAAGCTCTTTGACATCGTTTGGAACAGAAACATCAAACAGTGGTGTCTTACC
CCAAAGTAGTATGGTTGACTCTGCCTTAATACAGGATGCAAGATCTCTAAAAACACAGTTATCTCAAGGTCACTCAAGCC
CTCAATTAGACCCTTTGAGAAAAAGCCCAACCACTGAACAAGCAGTGAAGACTGTCTCGGCCCATTTACCTGCTCCAGCA
CCTGTTGGGAGAAGGAGCCCTGTATCAACTAGGCCTTTGCCATCTACCAGCCAAAAAGCAATAGAGATCAAGAGCACTGA
TGAGCTGAAGTACACAATGTTTCAAGACCAGAAAATGAGCAACTCAGAAATGATAGCAAGAGACAAGTAGCTCCAGGTAC
TCCTTCAGCTCCAACTTGAGGGCGTGGGGTTCAGCCGGGTAGCAGGGGAAGATTTGGTATTCTGCGAGATGGGCCAATGA
AATTTGAGAAAGACTTTGACTTTGAAAGTGCAAATGCACAATTCAACAAGGGAGAGATTGACAGAGAGTTTCATAATAAA
CTTAAAAGAAGATAAACTTGAGAAACAGGAGGAGCCTGTAAATGGTGAAGATAAAGGACCCAGGAGTTGATACCCCAAAA
GTAAAGGAAATGCTGATGAAGAAGATCCACTTGGACCTAACTGCTAGTTGGAAAAAACTAAATCCTTCTTTGATAATATT
TCTTGTGATGACAATAGGGAACGGATATCAACCTGGGCTGAAGAAAGAAGATTAAATGCTGAAACATTTGGAATCCCACT
TTGTCCAAATCGTGGCTGTGGGAGACGCAGAGGCAGAGGGATCTTTGGTTTCTGTGGTGGCAGAGGGCATGGTGGTAGCA
GATGTGGTACTTTAACCATCCCTGGAGGATTTCGCAGTGGATTCAGAGGAGGTCATGGGGGCAGGGAGTTTTCGGATTTC
GAATGTAGGAAA

Alignment

ORF - retro_pabe_2906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.24 %
• Parental protein coverage: 82.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CEPPKPQCSLPQDPAIVQSSLGSSTSSFQSMG-SYGPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTSF
          CEPPKPQCSLP.DPAI.QSSLGSSTSSF...G.S.GP.GRM..YS.FS.SSLVGQ.FGAV.VAGSSLTSF
Retrocopy CEPPKPQCSLPEDPAILQSSLGSSTSSFRCVG>SHGPLGRMIIYSRFSLSSLVGQEFGAVAVAGSSLTSF

Parental  GTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGRRS
          GTETSNSG.LPQSS.V.SA..QD.RSLKTQLSQG.SSPQLDPLRKSPT.EQAV.T.SAHLPAPA.VGRRS
Retrocopy GTETSNSGVLPQSSMVDSALIQDARSLKTQLSQGHSSPQLDPLRKSPTTEQAVKTVSAHLPAPAPVGRRS

Parental  PVSTRPLPSTSQKAGE-NPEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIR
          PVSTRPLPSTSQKA.E...EH..AEVH.VSRPENEQLRND.KRQVAPG.PSAP..GRG...G.RGRFGI.
Retrocopy PVSTRPLPSTSQKAIE<DQEH**AEVHNVSRPENEQLRNDSKRQVAPGTPSAPT*GRGVQPGSRGRFGIL

Parental  RDGPMKFEKDFDFESANAQFN-KEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEE
          RDGPMKFEKDFDFESANAQFN..E.....F.....LKEDKLEKQE.PVNGEDKG..............E.
Retrocopy RDGPMKFEKDFDFESANAQFN>RERLTESFI--INLKEDKLEKQEEPVNGEDKGPRS*YPKSKGNADEE-

Parental  DPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGFRGGRGRG
          DPLGPNC...KTKSFFDNISCDDNRER..TWAEERRLNAETFGIPL.PNRG.G..RGRG..GF.GGRG.G
Retrocopy DPLGPNC*LEKTKSFFDNISCDDNRERISTWAEERRLNAETFGIPLCPNRGCGRRRGRGIFGFCGGRGHG

Parental  GGRGGTFTAPRGFRGGFRGGRGGREFADFEYRK
          G.R.GT.T.P.GFR.GFRGG.GGREF.DFE.RK
Retrocopy GSRCGTLTIPGGFRSGFRGGHGGREFSDFECRK

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	47.05 RPM
SRP007412_cerebellum	0.00 RPM	77.34 RPM
SRP007412_heart	0.03 RPM	36.12 RPM
SRP007412_kidney	0.00 RPM	69.71 RPM
SRP007412_liver	0.00 RPM	35.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2906 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2906 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2378
Pan troglodytes	retro_ptro_2389
Macaca mulatta	retro_mmul_1860

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906 ,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,