RetrogeneDB ID: retro_ptro_3204

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:44761056..44761919(-)
• Located in intron of: ENSPTRG00000021820

Retrocopy information

• Ensembl ID: ENSPTRG00000011647
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RRM2B
• Ensembl ID: ENSPTRG00000020481
• Aliases: None
• Description: None

Sequence

>retro_ptro_3204
GATGAGCCGCTGCTGAGAGGAAACCCTTGCCGCTTTGTCATCTTCCCCGTCGAGTACCATGATATCTGGCAGATGTATAA
GAAGGCGGAGGCTTCCTTCTGGACCACCGAGGAGGTGGACCTGTCCAAGGACATTCGGCACTGGGAATCCCCGAAGCCCG
AGGAGAGATATTTTATATCCCATGTTCTGGTTTTCTTTGCAGCAAGTGATGGCATAGTAAATGAAAATTTGGTGGAGCGA
TTTAGCCAAATAGTTCAGATTACAGAAGCCCGCTGTTTCTATGGCTTCCAAATTGCCATGGAAAACATACATTCTGAAAT
GTATAGTCTCCTTATTGACACTTACATCAAAGATCCCAAAGAAAAGGAATTTCTCTTCAATGCCATTGAACGATGCCTTG
TGTCAAGAAGAAGGCAGATTGGGCCTTGTGCTGGATTGGGGACAAAGAGGCTACCTATGGTGAACGTGTTGTAGCCTTCG
CTGCAGTAGAAGGCATCTTCTTTTCTGGTTCTTTTGCATCGATATTCTGGCTCAAGAAACGAGGACCGATGCCTGGCCTC
ACGTTTTCCAATGAACTTATTAGCAGAGATGAGGGTTTACACTGTGATTTTGCTTGCTTGATGTTCAAACACCTGGTACA
CAAACCATCGGAGGAGAAAGTGAGAGAAATAATTATCAATGCTGTTCAGATAGAACAAGAATTCCTCACCGAGGCCTTGC
CTGTGAAGCTCATTGGGATGAATTGCACTCTAATGAAGCAATACATTGAGTTTGTGGCAGACAGACTTATGCTGGAACTG
GGTTTTAGCAAGGTTTTCGGAGTAGAGAGCCCATTTGACTTTACGGAGAATATTTCACTGAAA

Alignment

ORF - retro_ptro_3204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.93 %
• Parental protein coverage: 82.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASD
          .EPLLR....RFVIFP..Y.DIW.MYK.A.ASFWT.EEVDLSKD..HW...K..E.YFISH.L.FFAASD
Retrocopy DEPLLRGNPCRFVIFPVEYHDIWQMYKKAEASFWTTEEVDLSKDIRHWESPKPEERYFISHVLVFFAASD

Parental  GIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIE-TMPYVKKKA
          GIVNENLVERFSQ.VQ..EARCFYGFQI..EN.HSEMYSLLIDTYI.DPK..EFLFNAIE.TMP.VKKKA
Retrocopy GIVNENLVERFSQIVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEKEFLFNAIE<TMPCVKKKA

Parental  DWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMF
          DWAL.WI.D...T.GERVVAFAAVEG.FFSGSFA.IFWLKKRG.MPGLTFSNELISRDEGLHCDFACLMF
Retrocopy DWALCWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGPMPGLTFSNELISRDEGLHCDFACLMF

Parental  QYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPF
          ..LV.KPSEE.VREII..AV.IEQEFLTEALPV.LIGMNC.LMKQYIEFVADRL..ELGFSKVF..E.PF
Retrocopy KHLVHKPSEEKVREIIINAVQIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFSKVFGVESPF

Parental  DFMENISLE
          DF.ENISL.
Retrocopy DFTENISLK

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	0.02 RPM	23.76 RPM
SRP007412_cerebellum	0.11 RPM	28.11 RPM
SRP007412_heart	0.26 RPM	28.24 RPM
SRP007412_kidney	0.05 RPM	26.33 RPM
SRP007412_liver	0.23 RPM	7.82 RPM
SRP007412_testis	0.63 RPM	18.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3204 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3204 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4815
Gorilla gorilla	retro_ggor_3001
Pongo abelii	retro_pabe_3743
Macaca mulatta	retro_mmul_2568

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012265	4 retrocopies	retro_chof_1118, retro_chof_1233, retro_chof_277, retro_chof_692,
Callithrix jacchus	ENSCJAG00000015923	1 retrocopy	retro_cjac_4130,
Echinops telfairi	ENSETEG00000020338	1 retrocopy	retro_etel_1219,
Gorilla gorilla	ENSGGOG00000003053	1 retrocopy	retro_ggor_3001,
Mus musculus	ENSMUSG00000022292	1 retrocopy	retro_mmus_988,
Otolemur garnettii	ENSOGAG00000004487	1 retrocopy	retro_ogar_2602,
Pan troglodytes	ENSPTRG00000020481	1 retrocopy	retro_ptro_3204 ,
Ictidomys tridecemlineatus	ENSSTOG00000008543	2 retrocopies	retro_itri_1555, retro_itri_877,
Tupaia belangeri	ENSTBEG00000008855	1 retrocopy	retro_tbel_3693,