RetrogeneDB ID: retro_pabe_2270

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:174085962..174087287(+)
• Located in intron of: ENSPPYG00000014293

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP468F2127
• Ensembl ID: ENSPPYG00000004562
• Aliases: None
• Description: keratin, type II cytoskeletal 8 [Source:RefSeq peptide;Acc:NP_001127365]

Sequence

>retro_pabe_2270
CGAGTGAGCAGCAGCAGCTTCCGGGGTAGCCTGGGTGGAGGCTATGGTGAGGCCAGCGGCATAGGAGGCATCACCGCTGT
CACGTTCAACCAGAGCCTGCTGAGCCCTGTTAACCTGGAGGTGGATCCCAATATCCAGGCCATACACACCCAGGAGAAGG
AGCAGATCAAGACCCTCAACAACAAGTTTGCCTCCTTCATCGACAAGGTACGGTTCCTGCAGCAGCAGAACAAGATGCTG
GAGACCAAGTGGAGCCTCCTGCAGCAGCAGAAGATGGCTCGGATCAACATGTTTGAGAGCTACATGAACAACCTTAGGTG
GCAGCTGGAGGCTCTGGGCCAGGAGAAGCTGAAGCTGGAGGCGGAGCTTGGCAATATGCAGGGGGCTGGTGGAGGACTTC
AAGAACAAGTATGAGGATGAGATCAATAAGCGTACAGAAATGGAGAATGAATTTGTCCTCATCAAGAAGGACATGGATGA
AGCTTACATGAACAAGGTAGAGCTGGAGTCTCGCCTGGAAGGGCTGACTGATGAGATCAACTTCCTCAGGCAGCTGTATG
AAGAGGAGATCCAGGAGCTGCAGTCCCAGATCTCGGGCACGTCTGCGGTGCTGTCCATGGACAACAGCCGCTCCCTGGAC
ATGGACAGCATCATCGCTGAGGTCAAGGCACAGTAGGAGGACATCGCCAACTGCAGCTGGGCTGAGGCTGAGAGCATGTA
CCAGATCAAGTATGCAGAGCTGCAGACGCTGGCTGGGAAGCACGGGGATGACCTGCGGCGTACAAAGACTTAGATCTCCG
AGATGAACCGGAACATCAGCCGGCTCCAGGCTGAGATTGAGGGCCCCAAAGGCCAGAGGGCTTCCCTGGAGGCCCCCATC
GCAGATGCCGAGCAGCGTGGGGAGCTGGCCGTTAAGGATGCCAGCGCCAAGCTGTCGGAGCTGGAGGCCACCCTGCAGCG
GGCCAAGCAGGACATGGCGCGGCAGCTGCGTGAGTACCAGAAGCTGATGAACGTCAAACTGGCCCTGGACATGGAGATCA
CCAGCTACAGGAAGCTGCTGGAGGGCGAGGAGAGCCCGGCGGGAGTCTGGGATGCAGAACATGAGTATCCATATGAAGAC
CACTAGCGGCTATGCAGGTGGTCTGAGCTCCGCCTATGGGGGCCTCACAAGCCCTGGCCTCAGCTATGGCCTAAGCTCCA
GCTTTGGCTCTGTCGCGGACTCCAGCTCATTCAGCCGCACCAGCTCCGCTAGGGCCATGGTTGTGCAGAAGATTGAGACC
CGCGATGGGAAGCTGGTATCCGAGTCCTCTGACGTCCTGCCCAAG

Alignment

ORF - retro_pabe_2270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RISSSSSRVSSSFGLGGYG-GSGMGGITAVTVNQSL-SPV-LEVDPNI-AVRTQEKEQIKTLNNKFASFI
          R.SSSS.R.S.....GGYG..SG.GGITAVT.NQSL.SPV.LEVDPNI.A..TQEKEQIKTLNNKFASFI
Retrocopy RVSSSSFRGSLG---GGYGEASGIGGITAVTFNQSLLSPVNLEVDPNIQAIHTQEKEQIKTLNNKFASFI

Parental  DKVRFLEQQNKMLETKWSLLQQQKTARSNMDNMFESYINNLRRQLETLGQEKLKLEAELGNMQG-LVEDF
          DKVRFL.QQNKMLETKWSLLQQQK.AR....NMFESY.NNLR.QLE.LGQEKLKLEAELGNMQG.LVEDF
Retrocopy DKVRFLQQQNKMLETKWSLLQQQKMARI---NMFESYMNNLRWQLEALGQEKLKLEAELGNMQG>LVEDF

Parental  KNKYEDEINKRTEMENEFVLIKKDVDEAYMNKVELESRLEGLTDEINFLRQLYEEEIRELQSQISDTSVV
          KNKYEDEINKRTEMENEFVLIKKD.DEAYMNKVELESRLEGLTDEINFLRQLYEEEI.ELQSQIS.TS.V
Retrocopy KNKYEDEINKRTEMENEFVLIKKDMDEAYMNKVELESRLEGLTDEINFLRQLYEEEIQELQSQISGTSAV

Parental  LSMDNSRSLDMDSIIAEVKAQYEDIANRSRAEAESMYQIKYEELQSLAGKHGDDLRRTKTEISEMNRNIS
          LSMDNSRSLDMDSIIAEVKAQ.EDIAN.S.AEAESMYQIKY.ELQ.LAGKHGDDLRRTKT.ISEMNRNIS
Retrocopy LSMDNSRSLDMDSIIAEVKAQ*EDIANCSWAEAESMYQIKYAELQTLAGKHGDDLRRTKT*ISEMNRNIS

Parental  RLQAEIEGLKGQRASLEAAIADAEQRGELAIKDANAKLSELEAALQRAKQDMARQLREYQELMNVKLALD
          RLQAEIEG.KGQRASLEA.IADAEQRGELA.KDA.AKLSELEA.LQRAKQDMARQLREYQ.LMNVKLALD
Retrocopy RLQAEIEGPKGQRASLEAPIADAEQRGELAVKDASAKLSELEATLQRAKQDMARQLREYQKLMNVKLALD

Parental  IEIATYRKLLEGEES-RLESGMQNMSIHTKTTSGYAGGLSSAYGGLTSPGLSYGLGSSFGSGAGSSSFSR
          .EI..YRKLLEGEES.R.ESGMQNMSIH.KTTSGYAGGLSSAYGGLTSPGLSYGL.SSFGS.A.SSSFSR
Retrocopy MEITSYRKLLEGEES>RRESGMQNMSIHMKTTSGYAGGLSSAYGGLTSPGLSYGLSSSFGSVADSSSFSR

Parental  TSSSRAVVVKKIETRDGKLVSESSDLLPK
          TSS.RA.VV.KIETRDGKLVSESSD.LPK
Retrocopy TSSARAMVVQKIETRDGKLVSESSDVLPK

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	0.22 RPM	0.55 RPM
SRP007412_cerebellum	0.24 RPM	0.12 RPM
SRP007412_heart	0.00 RPM	23.57 RPM
SRP007412_kidney	0.00 RPM	106.83 RPM
SRP007412_liver	0.00 RPM	163.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2270 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2270 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2270 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2731
Gorilla gorilla	retro_ggor_1900
Macaca mulatta	retro_mmul_289

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 152 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007199	2 retrocopies	retro_cfam_1036, retro_cfam_1590,
Callithrix jacchus	ENSCJAG00000018147	3 retrocopies	retro_cjac_124, retro_cjac_167, retro_cjac_216,
Cavia porcellus	ENSCPOG00000002615	5 retrocopies	retro_cpor_1269, retro_cpor_1459, retro_cpor_233, retro_cpor_302, retro_cpor_516,
Dasypus novemcinctus	ENSDNOG00000007400	3 retrocopies	retro_dnov_1267, retro_dnov_1886, retro_dnov_2358,
Felis catus	ENSFCAG00000000298	2 retrocopies	retro_fcat_1142, retro_fcat_891,
Homo sapiens	ENSG00000170421	28 retrocopies	retro_hsap_1012, retro_hsap_1024, retro_hsap_1324, retro_hsap_1513, retro_hsap_1557, retro_hsap_1599, retro_hsap_169, retro_hsap_1708, retro_hsap_235, retro_hsap_2354, retro_hsap_2669, retro_hsap_2731, retro_hsap_2768, retro_hsap_2797, retro_hsap_2842, retro_hsap_3069, retro_hsap_3359, retro_hsap_3379, retro_hsap_3433, retro_hsap_371, retro_hsap_3963, retro_hsap_4203, retro_hsap_4688, retro_hsap_4691, retro_hsap_4775, retro_hsap_644, retro_hsap_844, retro_hsap_932,
Gorilla gorilla	ENSGGOG00000014673	18 retrocopies	retro_ggor_1160, retro_ggor_1787, retro_ggor_1862, retro_ggor_1897, retro_ggor_1900, retro_ggor_2320, retro_ggor_2662, retro_ggor_2913, retro_ggor_2918, retro_ggor_297, retro_ggor_2975, retro_ggor_382, retro_ggor_564, retro_ggor_66, retro_ggor_691, retro_ggor_751, retro_ggor_803, retro_ggor_809,
Macaca mulatta	ENSMMUG00000002163	22 retrocopies	retro_mmul_1069, retro_mmul_1122, retro_mmul_1178, retro_mmul_1349, retro_mmul_1351, retro_mmul_1412, retro_mmul_1697, retro_mmul_1753, retro_mmul_1810, retro_mmul_1855, retro_mmul_1866, retro_mmul_2097, retro_mmul_2137, retro_mmul_2357, retro_mmul_2431, retro_mmul_2546, retro_mmul_289, retro_mmul_488, retro_mmul_58, retro_mmul_766, retro_mmul_816, retro_mmul_886,
Mustela putorius furo	ENSMPUG00000006441	7 retrocopies	retro_mputfur_1101, retro_mputfur_1208, retro_mputfur_1271, retro_mputfur_1557, retro_mputfur_1587, retro_mputfur_556, retro_mputfur_895,
Mus musculus	ENSMUSG00000049382	1 retrocopy	retro_mmus_2905,
Nomascus leucogenys	ENSNLEG00000017733	8 retrocopies	retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Oryctolagus cuniculus	ENSOCUG00000006945	1 retrocopy	retro_ocun_313,
Otolemur garnettii	ENSOGAG00000011740	16 retrocopies	retro_ogar_1076, retro_ogar_1162, retro_ogar_1256, retro_ogar_1572, retro_ogar_1874, retro_ogar_1898, retro_ogar_1952, retro_ogar_2004, retro_ogar_2149, retro_ogar_2177, retro_ogar_2261, retro_ogar_2500, retro_ogar_3198, retro_ogar_3318, retro_ogar_339, retro_ogar_664,
Pongo abelii	ENSPPYG00000004548	1 retrocopy	retro_pabe_1103,
Pongo abelii	ENSPPYG00000004562	31 retrocopies	retro_pabe_1102, retro_pabe_1261, retro_pabe_1289, retro_pabe_1460, retro_pabe_1743, retro_pabe_2063, retro_pabe_2077, retro_pabe_2129, retro_pabe_2142, retro_pabe_2214, retro_pabe_2270 , retro_pabe_2352, retro_pabe_2544, retro_pabe_2741, retro_pabe_2763, retro_pabe_2787, retro_pabe_2842, retro_pabe_2926, retro_pabe_2943, retro_pabe_3138, retro_pabe_332, retro_pabe_3439, retro_pabe_3644, retro_pabe_3716, retro_pabe_417, retro_pabe_460, retro_pabe_569, retro_pabe_605, retro_pabe_701, retro_pabe_803, retro_pabe_851,
Pteropus vampyrus	ENSPVAG00000009360	3 retrocopies	retro_pvam_1299, retro_pvam_1396, retro_pvam_45,
Rattus norvegicus	ENSRNOG00000009779	1 retrocopy	retro_rnor_807,