RetrogeneDB ID: retro_pabe_1856

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:32529134..32530219(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTRC
• Ensembl ID: ENSPPYG00000002583
• Aliases: None
• Description: F-box/WD repeat-containing protein 1A [Source:RefSeq peptide;Acc:NP_001124974]

Sequence

>retro_pabe_1856
CAGATAAGTAATGGAACATCATTTGTGATCATCTCCAGAAAGAGGCCATCAGAAGGAAACTATCAAAAAGAAAAAGACTT
GTATATTCAATATTTTAACCAGTGGTCTGAATCAGATCAATTGGAATTTGTGGGACATCTTATTTCACAAATGTGTCATT
ATCAGCATGGACGTATTAACTCTTACCTGAAGCCCATGTTGCAGCAGGACTTTATTACTGCTTTACTCGAGCAAGGCTTA
AATCACATAGCAGAAAACACTCTTTCGTACCTGGATGCCAGGTCTCTGTGTGCAGCAGAGCTGGTATGTAAAGAATGGCA
GGGAGTGATCTCAGAACCAATGCTTTGGAAGAAGCTGATTGAACGAATGGTACACACTGATCCCCTATGGAAAGGACTTT
CAGAAGGAAGAGGGTGGGATCAGTACCTGTTTCAAAACAGACCCACAGCTAGCCCTCCAAATTCATTTTACAGGTCATTA
TACCCAAAGATTATCCAGGATATAGAGACTATAGAATCCACCTAGCGGTGTGGCTGACACAGCTTGCAGAGGATTCAGTA
CCGCTCTGAAAATAGTAAAGGTGTCTATGGTTTACAGTACGATGATGAAAAAATTATCAGTGGCCTACAAGATAATTATA
TTAAGATTTGGGATAAAACCAGCCTGGAATGTTTGAAAGTGTTAACGGCCACACAGGCTCTGTCCTCTGTCTGCAGTAGG
ATGAGCGTGTCATTGTAACTGGCTCTTCAGATTCTACGGTGAGAGTGTGGGAAGTGAACACGGGTGAAGTTCTTAACACA
TTAATCCACCACAGTGAGGATGTACTGCACTTACGCTTCAGCAGTGGACTGATGGTGACCTGTTCCAAGGACCGCTCCAT
TGCTGTGTGGGACATGGCTTCTGCGACCGATATCACTTTACGTGGTGTCCTGGTTGGCCACTGAGCTGCTGTCAACGTAG
TAGACTTTGACGAGAAATACATCGTGTCTGCCTCTGGTGACAGGACCATCAAAGTCTGGAGCATGAGCACCTGTGAATTT
GTTTGTACTCTCAATGGGCACAAGCGAGTCTTGTCTCTAGTACAG

Alignment

ORF - retro_pabe_1856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.62 %
• Parental protein coverage: 60.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLANGTSSMIVPKQRKLSASYEKEKELCVKYFEQWSESDQVEFVEHLISQMCHYQHGHINSYLKPMLQRD
          ...NGTS..I....R.....Y.KEK.L...YF.QWSESDQ.EFV.HLISQMCHYQHG.INSYLKPMLQ.D
Retrocopy QISNGTSFVIISRKRPSEGNYQKEKDLYIQYFNQWSESDQLEFVGHLISQMCHYQHGRINSYLKPMLQQD

Parental  FITALPARGLDHIAENILSYLDAKSLCAAELVCKEWYRVTSDGMLWRKLIERMVRTDSLWRGLAERRGWG
          FITAL...GL.HIAEN.LSYLDA.SLCAAELVCKEW..V.S..MLW.KLIERMV.TD.LW.GL.E.RGW.
Retrocopy FITALLEQGLNHIAENTLSYLDARSLCAAELVCKEWQGVISEPMLWKKLIERMVHTDPLWKGLSEGRGWD

Parental  QYLFKNKPPDGNAAPNSFYRALYPKIIQDIETIESNWRCGRHSLQRIHCRSETSKGVYCLQYDDQKIVSG
          QYLF.N.P......PNSFYR.LYPKIIQDIETIES..RCG.HSLQRI..RSE.SKGVY.LQYDD.KI.SG
Retrocopy QYLFQNRPTA--SPPNSFYRSLYPKIIQDIETIEST*RCG*HSLQRIQYRSENSKGVYGLQYDDEKIISG

Parental  LRDNTIKIWDKNTLECKRILT-GHTGSVLCLQYDERVIITGSSDSTVRVWDVNTGEMLNTLIHHCEAVLH
          L.DN.IKIWDK..LEC...LT.GHTGSVLCLQ.DERVI.TGSSDSTVRVW.VNTGE.LNTLIHH.E.VLH
Retrocopy LQDNYIKIWDKTSLECLKVLT<GHTGSVLCLQ*DERVIVTGSSDSTVRVWEVNTGEVLNTLIHHSEDVLH

Parental  LRFNNGMMVTCSKDRSIAVWDMASPTDITLRRVLVGHRAAVNVVDFDDKYIVSASGDRTIKVWNTSTCEF
          LRF..G.MVTCSKDRSIAVWDMAS.TDITLR.VLVGH.AAVNVVDFD.KYIVSASGDRTIKVW..STCEF
Retrocopy LRFSSGLMVTCSKDRSIAVWDMASATDITLRGVLVGH*AAVNVVDFDEKYIVSASGDRTIKVWSMSTCEF

Parental  VRTLNGHKRGIACLQ
          V.TLNGHKR.....Q
Retrocopy VCTLNGHKRVLSLVQ

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	1.44 RPM	118.82 RPM
SRP007412_cerebellum	3.28 RPM	97.28 RPM
SRP007412_heart	0.75 RPM	21.13 RPM
SRP007412_kidney	0.93 RPM	23.24 RPM
SRP007412_liver	0.64 RPM	16.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1856 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1856 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1576
Macaca mulatta	retro_mmul_1596

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013579	1 retrocopy	retro_meug_1243,
Pongo abelii	ENSPPYG00000002583	1 retrocopy	retro_pabe_1856 ,
Rattus norvegicus	ENSRNOG00000016280	1 retrocopy	retro_rnor_603,