RetrogeneDB ID: retro_ptro_666

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:10303087..10303687(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPAB
• Ensembl ID: ENSPTRG00000017601
• Aliases: None
• Description: Heterogeneous nuclear ribonucleoprotein A/B [Source:UniProtKB/TrEMBL;Acc:K7CPF8]

Sequence

>retro_ptro_666
GCCGAGGACGAACAGATCAAAGCCAGCAAGAACGAGGAGGACGCAGGAAAAATGCTCGTTGGTGGCCTGAGCTGGGATAC
CAGCAAAAAAGATTTAAAAGGCTATTTCCCTAAATTTGGAGAGGTCATTGACTGTACAATAAAAATGGATCCCAACATTG
GACGGGCAAGAGGGTTTGGGTTTATCCTGTTCAAAGATGCAACCAATGTGGAGAAGGTCCTAGAGCAGGAGTACAGGCTG
GATGTCCGTGTCATTGACCCTAAAAAGGCCATGGCTATGAAGAAGGACCCGGTGAAGAAAATCTTCGTCGAGGGTCTGAA
TCCTGAAGCCACTGAGGAAAAGATCAGGGAGTACTTTGGCGAGTTTGGGGAGATCGAGGCCATTGAAATTCCAGTGGATC
CAAAGTTGAACAAAAGACAAGGTTTTGTGTTTATCACCTTTAAAAAAGAAGAACCTGTGAAGAAAGTTCTGGAGAAAAAG
TTCCATACTATCAGTGGAAGTAAGCGTGAGATCACGGTGGCCCAGCCCAAAGAAGTTTATTGGCAGCAGCGGTATGGTTC
TGGGGACCGTGGAAACCACAACGGAGGGAACCGAGGCAGC

Alignment

ORF - retro_ptro_666 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.07 %
• Parental protein coverage: 70.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEGDQINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASV
          AE..QI.ASKNEEDAGKM.VGGLSWDTSKKDLK.YF.KFGEV.DCTIKMDPN.GR.RGFGFILFKDA..V
Retrocopy AEDEQIKASKNEEDAGKMLVGGLSWDTSKKDLKGYFPKFGEVIDCTIKMDPNIGRARGFGFILFKDATNV

Parental  EKVLDQKEHRLDGRVIDPKKAMAMKKDPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKLNKR
          EKVL.Q.E.RLD.RVIDPKKAMAMKKDPVKKIFV.GLNPEATEEKIREYFGEFGEIEAIE.P.DPKLNKR
Retrocopy EKVLEQ-EYRLDVRVIDPKKAMAMKKDPVKKIFVEGLNPEATEEKIREYFGEFGEIEAIEIPVDPKLNKR

Parental  RGFVFITFKEEEPVKKVLEKKFHTVSGSKCEIKVAQPKEVYQQQQYGSGGRGNRNRGNRGS
          .GFVFITFK.EEPVKKVLEKKFHT.SGSK.EI.VAQPKEVY.QQ.YGSG.RGN.N.GNRGS
Retrocopy QGFVFITFKKEEPVKKVLEKKFHTISGSKREITVAQPKEVYWQQRYGSGDRGNHNGGNRGS

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	23.88 RPM
SRP007412_cerebellum	0.00 RPM	40.26 RPM
SRP007412_heart	0.03 RPM	40.28 RPM
SRP007412_kidney	0.00 RPM	51.94 RPM
SRP007412_liver	0.00 RPM	153.98 RPM
SRP007412_testis	0.21 RPM	38.99 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_666 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_666 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_666 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_962
Pongo abelii	retro_pabe_821

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000241	2 retrocopies	retro_cfam_408, retro_cfam_412,
Homo sapiens	ENSG00000197451	1 retrocopy	retro_hsap_962,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405,
Macropus eugenii	ENSMEUG00000007909	2 retrocopies	retro_meug_169, retro_meug_246,
Myotis lucifugus	ENSMLUG00000003380	2 retrocopies	retro_mluc_2024, retro_mluc_2138,
Nomascus leucogenys	ENSNLEG00000015775	1 retrocopy	retro_nleu_1611,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
Pongo abelii	ENSPPYG00000016107	1 retrocopy	retro_pabe_821,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Pan troglodytes	ENSPTRG00000017601	1 retrocopy	retro_ptro_666 ,