RetrogeneDB ID: retro_pabe_3327

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:49813045..49813811(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDI1
• Ensembl ID: ENSPPYG00000002039
• Aliases: None
• Description: isopentenyl-diphosphate Delta-isomerase 1 [Source:RefSeq peptide;Acc:NP_001126068]

Sequence

>retro_pabe_3327
GCAGAGGACAGAACCCAAAAAGGCACACACCTGGGCTGCCTGGTGTTCAAGCTGGAGGCTGCTCAGTGTTCTAGGACAAA
TCTGACATTTTGTAACAATGCTTGAAATAAATACCAGCCATCTCTATGAGCAACAGGTTCAGCTCTTGGCAGACACGTGT
AACCTTATTGATGAAAATGACAATAAAATTGGGGCTGAGACCAAGAAGAATTGTCACCTGAATGAGAACACTGAAAAAGG
ATTATTGCATTGGACTTTTAGTGTCTTCTTATTCAACACCAAAAATAAGCTCCTGCTAGAGGAAAGCTCAGATGCTAAGA
TTTCCTTTCCAGGTTGTTTTACCAATACTTGTTGTGGTCATCCATTGGGTAATTCAGGCAAGCTTGAGGAAAGTGATGAC
CTTGAAGTAAGGCAAGCAGTGCAGAAGCATCTGAAAGCTGAGTTAGGAATCCCCATAGAAGTTCCTCCAGAAGAAATTAA
TTATTTAACATGAATTCACTATGAAGCTCAGTCTGATGGTATCTGGGGTGAACATGAAATTGATTACATTTTATTTGTGA
GGAAGAGTGTCACTTTGAGTCTAGATCCCAATGAGATTAAAAGCTATCTCAAAGGAAGAACTAGAAGAACTTCTGAAAAC
AGAAGCTACTTGTAAAATAAGAGAACACCATGGTTTCAAATTATTGTAGAGGCTTTTCTTATTAAATGGTGGGATAACTT
AAATCATTTGAATCAGTTTGTTTACCACAAGAAAATACATAGAATG

Alignment

ORF - retro_pabe_3327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.59 %
• Parental protein coverage: 91.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AADSAQSG-RAPGPAGVRGR-RLISVLGQIRHFVMMPEINTDHLDKQQVQLLAEMCILIDENDNKIGAET
          A.D..Q.G...PG..GV....RL.SVLGQI.HFV.M.EINT.HL..QQVQLLA..C.LIDENDNKIGAET
Retrocopy AEDRTQKG<HTPGLPGVQAG<RLLSVLGQI*HFVTMLEINTSHLYEQQVQLLADTCNLIDENDNKIGAET

Parental  KKNCHLNENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNPGELEENDALGVR
          KKNCHLNEN.EKGLLH..FSVFLFNT.NKLLL...SDAKI.FPGCFTNTCC.HPL.N.G.LEE.D.L.VR
Retrocopy KKNCHLNENTEKGLLHWTFSVFLFNTKNKLLLEESSDAKISFPGCFTNTCCGHPLGNSGKLEESDDLEVR

Parental  RAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPD-PNEIKSYCYV
          .A.Q..LKAELGIP.E.VPPEEINYLT.IHY.AQSDGIWGEHEIDYIL.VRK.VTL..D.P...K.....
Retrocopy QAVQKHLKAELGIPIE-VPPEEINYLT*IHYEAQSDGIWGEHEIDYILFVRKSVTLSLD>PMRLKA---I

Parental  SKEELKELLKKAASGEI-KITPWFKIIAETFLFKWWDNLNHLNQFVDHEKIYRI
          SKEEL.ELLK..A...I.K.TPWF.II.E.FL.KWWDNLNHLNQFV.H.KI.R.
Retrocopy SKEELEELLKTEATCKI<KRTPWFQIIVEAFLIKWWDNLNHLNQFVYHKKIHRM

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	25.38 RPM
SRP007412_cerebellum	0.00 RPM	17.88 RPM
SRP007412_heart	0.00 RPM	9.39 RPM
SRP007412_kidney	0.00 RPM	10.81 RPM
SRP007412_liver	0.00 RPM	27.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3327 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3327 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4053
Pan troglodytes	retro_ptro_2747
Gorilla gorilla	retro_ggor_2722

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008483	3 retrocopies	retro_cjac_2083, retro_cjac_2591, retro_cjac_2820,
Erinaceus europaeus	ENSEEUG00000012555	3 retrocopies	retro_eeur_188, retro_eeur_198, retro_eeur_61,
Homo sapiens	ENSG00000067064	3 retrocopies	retro_hsap_2161, retro_hsap_2444, retro_hsap_4053,
Gorilla gorilla	ENSGGOG00000000934	3 retrocopies	retro_ggor_1521, retro_ggor_1717, retro_ggor_2722,
Macaca mulatta	ENSMMUG00000017115	3 retrocopies	retro_mmul_2340, retro_mmul_632, retro_mmul_899,
Monodelphis domestica	ENSMODG00000005998	5 retrocopies	retro_mdom_1107, retro_mdom_1692, retro_mdom_1697, retro_mdom_1724, retro_mdom_547,
Mus musculus	ENSMUSG00000058258	4 retrocopies	retro_mmus_2032, retro_mmus_2660, retro_mmus_417, retro_mmus_552,
Nomascus leucogenys	ENSNLEG00000013594	3 retrocopies	retro_nleu_1810, retro_nleu_2777, retro_nleu_2804,
Oryctolagus cuniculus	ENSOCUG00000007493	1 retrocopy	retro_ocun_267,
Ochotona princeps	ENSOPRG00000008692	2 retrocopies	retro_opri_694, retro_opri_755,
Pongo abelii	ENSPPYG00000002039	2 retrocopies	retro_pabe_1783, retro_pabe_3327 ,
Pan troglodytes	ENSPTRG00000002239	3 retrocopies	retro_ptro_1412, retro_ptro_1647, retro_ptro_2747,
Ictidomys tridecemlineatus	ENSSTOG00000023260	1 retrocopy	retro_itri_118,
Tursiops truncatus	ENSTTRG00000011174	1 retrocopy	retro_ttru_255,