RetrogeneDB ID: retro_ptro_2571

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:136616247..136617345(+)
• Located in intron of: ENSPTRG00000019722

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF14
• Ensembl ID: ENSPTRG00000017356
• Aliases: None
• Description: None

Sequence

>retro_ptro_2571
CTATCTGCTCTATGGGAAGAACACCCTGGCAGCGTGATCCCGTTTGCCTGGATGCAATTTCTTAAGGAAGAGACCCTAGT
ATACCTGAATATTGTCTCTCCTTTTGAGCTCAAGATTGATTCTCAGAAAAAAAGTGCAGAGAAGGACAGCTCAAGCCTCT
CCCAACACAGAGCTAGATTTTGGAGGAACTTCTGGATCTGATACAGACCAAGAGGAAACTGTGGATGAGACAGCTGTGTG
CAGGATGTGGAATCATTGTTAAATATGATCCAGGAAATCTTGGACTTTGATCAAGCTCAGCAGATAAAATGCTTTAATAG
TAATTTGTTCCTGTGCAATATCTGTTTCTGTAAGAAGCTGGGTAGTGAATGCATGTACTTCTTGGAGTGCAGGCATGTGT
ACTGCAAAGACTGTCTGAAGGACTACTTTGAAATCCAGATCAGAGATGGCCAGGTTCAATGCCTCAACTGCCCAGAACCA
AAGTGCCCTTCAGTGGCCACTACTGGTCAGGTCAAAGAGCTAGTGGAAGCAGAGTTATTTGCCTATTATGACTGCCTTCT
CCTCCAGTCCACCTTGGACCTGATGGCAGATGTGGCGTACTGCCCCCACGCGTGCTGCCAGCTGCCTGTGATGCAGGAGC
CTGGCTACATCATGGGTATCTGCTCCAGCTGCAATTTTGCCTTCTGTACCTTGTGCAGGTTGACCTACCATGGGGTCTCT
CCATGTAAGGTGACTGCAGAGAAATTAATAGACCTACGAAATGAATACCTGCAAGCAGATAAGGCCAATAAAAGACTTTT
GGAACAAAGGTATGATAAGAGGGTGATTCAGAAGGCACTGGAAGAGATGGAAAGTAAGGAGTGGCTAGAGAAAAACTTCA
AGAACTGCCCATGTTGTGGAACTCCCAGAGAGAAATTAGGTGGATATAACAAGATGACATGTACTGGCTGTATGCAATAT
TTCTGTTGGATTTGCATGAGTTCTCTCTCTAGAGCAAACCCTTACAAACATTTCACTGATCCTGCTTCAACACGTCTTAA
ACAGCTGTTTTATGCTGTGGATGTTGATGAAGATATTTGGGAAGATGAGATTGAAGAC

Alignment

ORF - retro_ptro_2571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.33 %
• Parental protein coverage: 77. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDNLWEEHRGSVVLFAWMQFLKEETLAYLNIVSPFELKIGSQKK-VQRRTAQASPNTELDFGGAAGSDVD
          L..LWEEH.GSV..FAWMQFLKEETL.YLNIVSPFELKI.SQKK.VQRRTAQASPNTELDFGG..GSD.D
Retrocopy LSALWEEHPGSVIPFAWMQFLKEETLVYLNIVSPFELKIDSQKK>VQRRTAQASPNTELDFGGTSGSDTD

Parental  -QEEIVD-ERAVQDVESLSNLIQEILDFDQAQQIKCFNSKLFLCNICFCEKLGSECMYFLECRHVYCKAC
          ..E........VQDVESL.N.IQEILDFDQAQQIKCFNS.LFLCNICFC.KLGSECMYFLECRHVYCK.C
Retrocopy QEETVDE<DSCVQDVESLLNMIQEILDFDQAQQIKCFNSNLFLCNICFCKKLGSECMYFLECRHVYCKDC

Parental  LKDYFEIQIRDGQVQCLNCPEPKCPSVATPGQVKELVEAELFARYDRLLLQSSLDLMADVVYCPRPCCQL
          LKDYFEIQIRDGQVQCLNCPEPKCPSVAT.GQVKELVEAELFA.YD.LLLQS.LDLMADV.YCP..CCQL
Retrocopy LKDYFEIQIRDGQVQCLNCPEPKCPSVATTGQVKELVEAELFAYYDCLLLQSTLDLMADVAYCPHACCQL

Parental  PVMQEPGCTMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLMDLRNEYLQADEANKRLLDQRYGKRVIQK
          PVMQEPG..MGICSSCNFAFCTLCRLTYHGVSPCKVTAEKL.DLRNEYLQAD.ANKRLL.QRY.KRVIQK
Retrocopy PVMQEPGYIMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLIDLRNEYLQADKANKRLLEQRYDKRVIQK

Parental  ALEEMESKEWLEKNSKSCPCCGTPIEKLDGCNKMTCTGCMQYFCWICMGSLSRANPYKHFNDPGSPCFNR
          ALEEMESKEWLEKN.K.CPCCGTP.EKL.G.NKMTCTGCMQYFCWICM.SLSRANPYKHF.DP.S.....
Retrocopy ALEEMESKEWLEKNFKNCPCCGTPREKLGGYNKMTCTGCMQYFCWICMSSLSRANPYKHFTDPASTRLKQ

Parental  LFYAVDVDDDIWEDEVED
          LFYAVDVD.DIWEDE.ED
Retrocopy LFYAVDVDEDIWEDEIED

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	0.07 RPM	38.91 RPM
SRP007412_cerebellum	0.00 RPM	45.74 RPM
SRP007412_heart	0.12 RPM	43.11 RPM
SRP007412_kidney	0.03 RPM	55.00 RPM
SRP007412_liver	0.07 RPM	23.04 RPM
SRP007412_testis	0.32 RPM	74.72 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2571 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2571 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3790
Pongo abelii	retro_pabe_3095
Macaca mulatta	retro_mmul_1647

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007803	1 retrocopy	retro_dnov_332,
Dasypus novemcinctus	ENSDNOG00000024423	1 retrocopy	retro_dnov_1704,
Homo sapiens	ENSG00000013561	2 retrocopies	retro_hsap_3790, retro_hsap_3881,
Gorilla gorilla	ENSGGOG00000008542	1 retrocopy	retro_ggor_2612,
Macaca mulatta	ENSMMUG00000009768	2 retrocopies	retro_mmul_1647, retro_mmul_934,
Pongo abelii	ENSPPYG00000015894	2 retrocopies	retro_pabe_3095, retro_pabe_3115,
Pan troglodytes	ENSPTRG00000017356	2 retrocopies	retro_ptro_2571 , retro_ptro_2643,