RetrogeneDB ID: retro_ptro_740

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:16270773..16271494(-)
• Located in intron of: ENSPTRG00000004735

Retrocopy information

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

Parental gene information

• Parental gene symbol: EGLN3
• Ensembl ID: ENSPTRG00000006250
• Aliases: None
• Description: None

Sequence

>retro_ptro_740
ATGCTCCTGGGACACATCATGAGGCAGGAATTGGAGAAAATTTCCCTAGAGTACATCATGCGCTGTCTGCGGGAAGTCAG
CTTCTGCTACCCGCAAAACTTCCTGGGCAAGGAGGTGGTGGGCAACTGCATCCAGGAGCACATTAAACAGCTGCATTGCA
AGGGGGCCCTGCGGGACAGCCAGCTGGCTGGGATGTGTGCAGTGTCTCTAAAGGGTGAACTGTGGGGTGATCAGTTCACC
CCACAGTTCTGGGAGCAACAAGAAGGGCTGCAAGGCCATTAGCTTCCTCCTGTCCCTCACTGACAGGCTGGTCCTCTAGT
GCAGGAGCCACTGGGAAAATACTATGTCAAGGAGAGGTCCAAGGCAATGGTGGCTTGCTATCTTAAAAATGGAATAGGTT
ACATTCATCATGTGGACACCTCAACAACGATGGCTGCTGCACCACCTGCATCTACTATCTGAACAAGAATTGGGATACCA
GGCTACACGGTGGGATCCTATGGCTATTTTCAGAGGAGAAATCATTCGTGGCAGATGTGGAGGCCAATTGTGAAAAAGTC
CTGCTCTCCTGGTCAGATTGCAGGAACCTACACGAGGTGCTGTCTTCCTATGAGACCAGATGTGCTATACTGTTTGGTAC
TTTGATAATGAAGAAAGGACAGAAGCCAAAAAGAAATTCAGGAATTTAATTAGGAAACATCTGCCCTCACTGAAGATTGA
C

Alignment

ORF - retro_ptro_740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPLGHIMRLDLEKIALEYIVPCLHEVGFCYLDNFLG-EVVGDCVLERVKQLHCTGALRDGQLAGPRAGVS
          M.LGHIMR..LEKI.LEYI..CL.EV.FCY..NFLG.EVVG.C..E..KQLHC.GALRD.QLAG..A...
Retrocopy MLLGHIMRQELEKISLEYIMRCLREVSFCYPQNFLGKEVVGNCIQEHIKQLHCKGALRDSQLAGMCAVSL

Parental  KRHLRGDQIT-WIGGNEEGCE-AISFLLSLIDRLVLYCGSR-LGKYYVKERSKAMVACYPGNGTGYVRHV
          K..L.GDQ.T.......EG...AISFLLSL.DRLVL.C.S..LGKYYVKERSKAMVACY..NG.GY..HV
Retrocopy KGELWGDQFTPQFWEQQEGLQ>AISFLLSLTDRLVL*CRSH<LGKYYVKERSKAMVACYLKNGIGYIHHV

Parental  DNP-NGDGRCITCIYYLNKNWDAKLHGGILRIFPEGKSFIADVEPIFDRLLFFWSDRRNPHEVQPSYATR
          D...N.DG.C.TCIYYLNKNWD..LHGGIL..F.E.KSF.ADVE......L..WSD.RN.HEV..SY.TR
Retrocopy DTS<NNDGCCTTCIYYLNKNWDTRLHGGILWLFSEEKSFVADVEANCEKVLLSWSDCRNLHEVLSSYETR

Parental  YAM-TVWYFDAEERAEAKKKFRNLTRKTESALTED
          .A..TVWYFD.EER.EAKKKFRNL.RK....L..D
Retrocopy CAI<TVWYFDNEERTEAKKKFRNLIRKHLPSLKID

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	10.30 RPM
SRP007412_cerebellum	0.00 RPM	4.23 RPM
SRP007412_heart	0.03 RPM	98.72 RPM
SRP007412_kidney	0.00 RPM	4.45 RPM
SRP007412_liver	0.00 RPM	5.70 RPM
SRP007412_testis	0.00 RPM	2.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_740 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_740 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1088
Pongo abelii	retro_pabe_906
Macaca mulatta	retro_mmul_845

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000129521	1 retrocopy	retro_hsap_1088,
Macaca mulatta	ENSMMUG00000000040	1 retrocopy	retro_mmul_845,
Oryctolagus cuniculus	ENSOCUG00000008560	1 retrocopy	retro_ocun_1902,
Pongo abelii	ENSPPYG00000005732	1 retrocopy	retro_pabe_906,
Pan troglodytes	ENSPTRG00000006250	1 retrocopy	retro_ptro_740 ,