RetrogeneDB ID: retro_pabe_2476

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:150354989..150356506(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPD1
• Ensembl ID: ENSPPYG00000013046
• Aliases: None
• Description: 60 kDa heat shock protein, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001127086]

Sequence

>retro_pabe_2476
TTATTGAGCAGACAGAGCTGGGGAAGTCCTAAAGTAACAAAAGATGGTGTGACTGTTGCAAAGTCAATTGACTTAAAGGA
TAAATATAAAAATACTGGAGCTAAACTTGTTCAAGATGTTGCCAATAACACAAATGAAGAGGCTGTGGATGGCACTACCA
CTGTTACTGCACTGGCACGCTCTATTGCCAAGGAAGGCTTTGAGAAGATTAGCAAAGGTACTAATCCGGTGGAAATCAGG
AGAGGTGTGATGTTAGCTGTTGGTGCTATAATCGCTGAACTAAAAAAGCAGTCTAAACTTGTGACCACCCCTGAAGAAAC
TGCACGGGTTGCTACAATTTCTGCAAATGGAGACAAAGAAATTGGCAATATCATCTCTGATGCAAAGAAAAAGGTTGGAA
GCAAAGGTATCATCACAGTAAATAATGGGAAAAGTACTGAATGATGAATTGGAAATTATTGAAGGCATGAAGTTTGATTG
AGGCTATATTTCTCCATACTTAATTAATACATCAAAAGGTCAGAAATGTGAATTCCAGGATGCCTATGTTCTGCTGAGTG
AGAAGAAAATTTCTAGTGTCCAGTCCATTGTACCTGCTCTTGAAATTGCCAATGCTTACTGTAAGCCTTGGTCATAATTG
CTGAAGACGTTAATGGAGAAGCTCTAAGTACACTCGTCTTGAATAGGCTAAAGGTTGGTCTTCAGGTTGTGGCAGTCAAG
GATCCAGGGTTTGGTGACAATAGAAACAACCAGCTTAAAGATATGGCTATTGTTACTAGTGGTGCAGTGTTTGCAGAAGA
GGGGTTGACCCTAAATCTGGACGTTCAGCCTCATGACTTAGGAAAAGTTGGAAAGGTCATTGTGACCAAAGAGGATGCCA
TGCTTTTAAAAGGAAAAGGTGACAAGGCTCAAATTGAAAATTGTGTTCAAGAAACTATTGAGCAGTTAGATGTCACAACT
AGTGAATATGAAAAGGAAAAACTGAATGAACACAGGCAAAACTTTCAGATGGAGTAGTTATGCTGAAGGTTGGTGGGACA
AGTGATGCTGAAGTGAATGAAAAGAAAGACAGAGTTACAGATGCCCTTAATGCTACAAGAGCTGCTGTTGAAGAAGGCAT
TGTTTTGAGAGGGGGTCGTGCCCTGGTTCGGTGCATTCCAGCCTTAGACTCATTGATTCCAGTTAATGAAGATCAAAACA
TTGGTAAATAAATTATTAAAAGAACATTCAAATTTCCAGCAATGACCATTGCTAAGAATGCAGGTGTTGAAGTATCTTTG
ATAGTTGAGAAAATTATGCAAAGTTCCTCAGAACTTGGTTATGATGCTATGGTCAGAGATTTTGTGAATATGGTGGAAAA
AAGAATTATTGATGCAACAAAGGTTGTGAGAACTGCTTTATTGGATGCTTCTGGTGTGGCCTCTCTCTTAACTACAGCAG
AAGTTGTAGTCACAGAAATTCCTAAAGAAGAGAAGGATCCTGGAATGGGTGCAATGGATGGAATGGGAGGTGGTATG

Alignment

ORF - retro_pabe_2476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 88.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VIIEQSWGSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKI
          ....QSWGSPKVTKDGVTVAKSIDLKDKYKN.GAKLVQDVANNTNEEA.DGTTT.T.LARSIAKEGFEKI
Retrocopy LLSRQSWGSPKVTKDGVTVAKSIDLKDKYKNTGAKLVQDVANNTNEEAVDGTTTVTALARSIAKEGFEKI

Parental  SKGANPVEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITV
          SKG.NPVEIRRGVMLAV.A.IAELKKQSK.VTTPEE.A.VATISANGDKEIGNIISDA.KKVG.KG.ITV
Retrocopy SKGTNPVEIRRGVMLAVGAIIAELKKQSKLVTTPEETARVATISANGDKEIGNIISDAKKKVGSKGIITV

Parental  KDGKT-LNDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKP
          ..GK..LNDELEIIEGMKFD.GYISPY.INTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANA..KP
Retrocopy NNGKS>LNDELEIIEGMKFD*GYISPYLINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAYCKP

Parental  -LVIIAEDVDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQP
          .LVIIAEDV.GEALSTLVLNRLKVGLQVVAVK.PGFGDNR.NQLKDMAI.T.GAVF.EEGLTLNL.DVQP
Retrocopy <LVIIAEDVNGEALSTLVLNRLKVGLQVVAVKDPGFGDNRNNQLKDMAIVTSGAVFAEEGLTLNL-DVQP

Parental  HDLGKVGEVIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERL-AKLSDGVAVLKVGG
          HDLGKVG.VIVTK.DAMLLKGKGDKAQIE...QE.IEQLDVTTSEYEKEKLNE...AKLSDGV..LKVGG
Retrocopy HDLGKVGKVIVTKEDAMLLKGKGDKAQIENCVQETIEQLDVTTSEYEKEKLNEHR<AKLSDGVVMLKVGG

Parental  TSDVEVNEKKDRVTDALNATRAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIKRTLKIPAMT
          TSD.EVNEKKDRVTDALNATRAAVEEGIVL.GG.AL.RCIPALDSL.P.NEDQ.IG..IIKRT.K.PAMT
Retrocopy TSDAEVNEKKDRVTDALNATRAAVEEGIVLRGGRALVRCIPALDSLIPVNEDQNIGK*IIKRTFKFPAMT

Parental  IAKNAGVEGSLIVEKIMQSSSEVGYDAMVGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTE
          IAKNAGVE.SLIVEKIMQSSSE.GYDAMV.DFVNMVEK.IID.TKVVRTALLDA.GVASLLTTAEVVVTE
Retrocopy IAKNAGVEVSLIVEKIMQSSSELGYDAMVRDFVNMVEKRIIDATKVVRTALLDASGVASLLTTAEVVVTE

Parental  IPKEEKDPGMGAMGGMGGGM
          IPKEEKDPGMGAM.GMGGGM
Retrocopy IPKEEKDPGMGAMDGMGGGM

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	98.36 RPM
SRP007412_cerebellum	0.00 RPM	94.97 RPM
SRP007412_heart	0.03 RPM	108.97 RPM
SRP007412_kidney	0.03 RPM	263.12 RPM
SRP007412_liver	0.06 RPM	241.60 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2476 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2476 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2987
Gorilla gorilla	retro_ggor_2069

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013770	1 retrocopy	retro_amel_771,
Canis familiaris	ENSCAFG00000010865	4 retrocopies	retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus	ENSCJAG00000003990	6 retrocopies	retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi	ENSETEG00000009184	4 retrocopies	retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens	ENSG00000144381	7 retrocopies	retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla	ENSGGOG00000008267	6 retrocopies	retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana	ENSLAFG00000000053	1 retrocopy	retro_lafr_476,
Macropus eugenii	ENSMEUG00000011987	2 retrocopies	retro_meug_1688, retro_meug_224,
Myotis lucifugus	ENSMLUG00000000871	4 retrocopies	retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta	ENSMMUG00000010489	1 retrocopy	retro_mmul_83,
Monodelphis domestica	ENSMODG00000012289	3 retrocopies	retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furo	ENSMPUG00000007818	3 retrocopies	retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus	ENSMUSG00000025980	5 retrocopies	retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439, retro_mmus_706,
Nomascus leucogenys	ENSNLEG00000006874	7 retrocopies	retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii	ENSOGAG00000034053	5 retrocopies	retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii	ENSPPYG00000013046	5 retrocopies	retro_pabe_2040, retro_pabe_2244, retro_pabe_2476 , retro_pabe_2887, retro_pabe_848,
Rattus norvegicus	ENSRNOG00000014525	9 retrocopies	retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Xenopus tropicalis	ENSXETG00000007509	1 retrocopy	retro_xtro_63,