RetrogeneDB ID: retro_ptro_2747

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:45945804..45946573(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDI1
• Ensembl ID: ENSPTRG00000002239
• Aliases: None
• Description: isopentenyl-diphosphate delta isomerase 1 [Source:HGNC Symbol;Acc:5387]

Sequence

>retro_ptro_2747
GCAGAGGACAGAACCCAAAAAGGCACACACCTGGGCTGCCTGGTGTTCAAGCTGGAGGCTGCTCAGTGTTCTAGGACAAA
TCTGACACTTTGTAACAATGCTTGAAATAAACACCAGCCATCTCTATGAGCAACAGGTTCAGCTCTTGGCAGACACATGT
AACCCTATTGATGAAAATGACAATAAAATTGGGGCTGAGACCGAGAAGAATTGTCACCTGAATGAGAACACTGAAAGAGG
ATTATTGCATTGGACTTTTAGTGTCTTCTTATTCAACACCAAAAATAAGCTCCTGCTAGAGGAAAGCTCATATGCTAAGA
TTTCCTTTCCGGGTTGCTTTACCAATACTTGTTGTGGTCATCCATTAGGTAATTCAGGCAAGCTTGAGGAAAGTGATGAC
CTTGAAGTAAGGCAAGCAGTGCAGAAGCATCTGAAAGCTGAGTTAGGAATCCCCATAGAAGCAGTTCCTCCAGAAGAAAT
TAATTATTTAACATGAATTCACTATGAAGCTCAGTCTGATGGTATCTGGGGTGAACACGAAATTGATTACATTTTATTTG
TGAGGAAGAATGTCACTTTGAGTCTAGATCCCAATGAGATTAAAAGCTATCTCAAAGGAAGAACTAGAAGAACTTCTGAA
AACAGCAGCTACTCGTAAAATAAGAGAACATCATGGTTTCAAATTATTGTAGAGGCTTTTCTTATTAAACGGTGGGATAA
CTTAAATCATTTGAATCAGTTTGTTTACCACAAGAAAATACATAGAATG

Alignment

ORF - retro_ptro_2747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.7 %
• Parental protein coverage: 91.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AADCAQSG-RSPGPAGV-CGRRLISVLEQIRHFVMMPEINTNHLDKQQVQLLAEMCILIDENDNKIGAET
          A.D..Q.G...PG..GV....RL.SVL.QI.HFV.M.EINT.HL..QQVQLLA..C..IDENDNKIGAET
Retrocopy AEDRTQKG<HTPGLPGV<SSWRLLSVLGQI*HFVTMLEINTSHLYEQQVQLLADTCNPIDENDNKIGAET

Parental  KKNCHLNENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNPAELEESDALGVR
          .KNCHLNEN.E.GLLH..FSVFLFNT.NKLLL...S.AKI.FPGCFTNTCC.HPL.N...LEESD.L.VR
Retrocopy EKNCHLNENTERGLLHWTFSVFLFNTKNKLLLEESSYAKISFPGCFTNTCCGHPLGNSGKLEESDDLEVR

Parental  RAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPD-PNEIKSYCYV
          .A.Q..LKAELGIP.E.VPPEEINYLT.IHY.AQSDGIWGEHEIDYIL.VRKNVTL..D.P...K.....
Retrocopy QAVQKHLKAELGIPIEAVPPEEINYLT*IHYEAQSDGIWGEHEIDYILFVRKNVTLSLD>PMRLKA---I

Parental  SKEELKELLKKAASGEI-KITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM
          SKEEL.ELLK.AA...I.K.T.WF.II...FL.K.WDNLNHLNQFV.H.KI.RM
Retrocopy SKEELEELLKTAATRKI<KRTSWFQIIVEAFLIKRWDNLNHLNQFVYHKKIHRM

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	13.80 RPM
SRP007412_cerebellum	0.00 RPM	13.80 RPM
SRP007412_heart	0.00 RPM	7.61 RPM
SRP007412_kidney	0.00 RPM	7.56 RPM
SRP007412_liver	0.00 RPM	8.71 RPM
SRP007412_testis	0.00 RPM	12.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2747 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2747 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4053
Gorilla gorilla	retro_ggor_2722
Pongo abelii	retro_pabe_3327

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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,