RetrogeneDB ID: retro_pabe_3508

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:122275569..122275943(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC15
• Ensembl ID: ENSPPYG00000005323
• Aliases: None
• Description: dnaJ homolog subfamily C member 15 [Source:RefSeq peptide;Acc:NP_001127291]

Sequence

>retro_pabe_3508
CAGCCAGACGCAGATATCATCCAGCAGGGACTGGCAAGAACTGTGACAGCTGCAGGGCTGGGTGCTGCTGCTCTTGCCTT
TGCAGGTCGCTGTGCGTCGCAGTCCTGGAAACCTCTAGAACAAGGATCACACAAGCAGTAGAGAACCTTTGAACTCCTAG
TGTTTCATCCTATTACAAAGGAGGATTTGAACAGAAAATGAGTAGGAGAAAAGCTAGTGTTATTTTAGGTGTAAGTTCAC
CTGCTGGCAAGGCTAAGATTAGAGCAGCTAATAGGAGAATCGTGATTTTGAATCACCCAGATGAAGGTGGATCTCCCTAC
TTAGCAACCAAAATAAATGAAACAGAAGATTTGCGAGAAGCGACCACCAATCAT

Alignment

ORF - retro_pabe_3508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.89 %
• Parental protein coverage: 83.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RPDADVDQQGLVRSLIAVGLGVAAFAFAGRYAFRIWKPLEQV-ITETAKKISTPSLSSYYKGGFEKKMSR
          .PDAD..QQGL.R...A.GLG.AA.AFAGR.A...WKPLEQ..IT.......TPS.SSYYKGGFE.KMSR
Retrocopy QPDADIIQQGLARTVTAAGLGAAALAFAGRCASQSWKPLEQG<ITQAVENL*TPSVSSYYKGGFEQKMSR

Parental  REAW-SYFRCP-SPSAGKAKIRTAHRRVMILNHPDKGGSPYVAAKINEAKDLLETTTKH
          R.A...YFRC..SP.AGKAKIR.A.RR..ILNHPD.GGSPY.A.KINE..DL.E.TT.H
Retrocopy RKAS<CYFRCK>SP-AGKAKIRAANRRIVILNHPDEGGSPYLATKINETEDLREATTNH

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	13.21 RPM
SRP007412_cerebellum	0.00 RPM	11.07 RPM
SRP007412_heart	0.00 RPM	19.18 RPM
SRP007412_kidney	0.00 RPM	22.27 RPM
SRP007412_liver	0.00 RPM	13.22 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3508 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3508 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3508 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4312
Pan troglodytes	retro_ptro_2920
Gorilla gorilla	retro_ggor_2882
Macaca mulatta	retro_mmul_1169
Callithrix jacchus	retro_cjac_634

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034785	1 retrocopy	retro_btau_1624,
Canis familiaris	ENSCAFG00000004664	1 retrocopy	retro_cfam_939,
Callithrix jacchus	ENSCJAG00000017589	2 retrocopies	retro_cjac_1663, retro_cjac_634,
Cavia porcellus	ENSCPOG00000003485	1 retrocopy	retro_cpor_327,
Equus caballus	ENSECAG00000007757	1 retrocopy	retro_ecab_561,
Erinaceus europaeus	ENSEEUG00000008785	5 retrocopies	retro_eeur_360, retro_eeur_608, retro_eeur_64, retro_eeur_93, retro_eeur_95,
Felis catus	ENSFCAG00000022632	1 retrocopy	retro_fcat_259,
Homo sapiens	ENSG00000120675	2 retrocopies	retro_hsap_3331, retro_hsap_4312,
Gorilla gorilla	ENSGGOG00000016338	2 retrocopies	retro_ggor_1294, retro_ggor_2882,
Loxodonta africana	ENSLAFG00000004343	2 retrocopies	retro_lafr_287, retro_lafr_942,
Myotis lucifugus	ENSMLUG00000008684	3 retrocopies	retro_mluc_1358, retro_mluc_1544, retro_mluc_520,
Macaca mulatta	ENSMMUG00000013689	1 retrocopy	retro_mmul_1169,
Mustela putorius furo	ENSMPUG00000001704	1 retrocopy	retro_mputfur_1065,
Nomascus leucogenys	ENSNLEG00000001759	4 retrocopies	retro_nleu_1408, retro_nleu_1464, retro_nleu_1675, retro_nleu_585,
Oryctolagus cuniculus	ENSOCUG00000001696	4 retrocopies	retro_ocun_1101, retro_ocun_487, retro_ocun_882, retro_ocun_936,
Ochotona princeps	ENSOPRG00000016191	5 retrocopies	retro_opri_1038, retro_opri_235, retro_opri_285, retro_opri_756, retro_opri_766,
Pongo abelii	ENSPPYG00000005323	1 retrocopy	retro_pabe_3508 ,
Pongo abelii	ENSPPYG00000014328	2 retrocopies	retro_pabe_2126, retro_pabe_44,
Pan troglodytes	ENSPTRG00000005831	2 retrocopies	retro_ptro_2148, retro_ptro_2920,
Pteropus vampyrus	ENSPVAG00000011281	1 retrocopy	retro_pvam_807,
Sorex araneus	ENSSARG00000007683	1 retrocopy	retro_sara_658,
Ictidomys tridecemlineatus	ENSSTOG00000012805	1 retrocopy	retro_itri_1710,
Taeniopygia guttata	ENSTGUG00000012364	2 retrocopies	retro_tgut_20, retro_tgut_45,
Tursiops truncatus	ENSTTRG00000015580	1 retrocopy	retro_ttru_1021,
Vicugna pacos	ENSVPAG00000001445	1 retrocopy	retro_vpac_113,