RetrogeneDB ID: retro_pabe_820

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:9193285..9194041(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT19
• Ensembl ID: ENSPPYG00000008416
• Aliases: None
• Description: keratin, type I cytoskeletal 19 [Source:RefSeq peptide;Acc:NP_001126058]

Sequence

>retro_pabe_820
GGTGAGCTGAAGGTGAAGATTCGCTACTGGGACCACAAGCAGGGGCCCGGGCCCCCGGCAATTACAGCCACTACTTCAAG
ACCCATCGAAGACCTGCGGGACAAGATTCTTGGTGTCACCACTGAGAACTCCAGGATTGTCTTGCAGACCGACAACCCCC
GCCTGGCTGCAGATCACTTCCGAACCAAGTCTGAGGTGGAGCAGGCTCTGCGAAGGAGCTTGGAGGCAGACATCAAGGCC
TGCGGCAGGGCGCCCGATGAGCTGACCCCAGCCAGGGCTCACCTGAAGACGCACATCCAAGACCTGCAGGAGGAGCTGGA
TCACCTGGAGAAGAACCACAACGAGGAAATCAGGGCTGCGGGTGGCCAGGTCAGTGTGGAGGTGGATTCTGCTCCAGGCT
TTTGTCTTGCCAAGATCCTGGGCAACACATGAAGCCAGTATGCGGTCTTGGCTGAGCAGATGCGGAAGATGCTGAAGCCT
GGTCACCAGCCAGACTGAGGAGCTGAGCTGGGAGGTCGCTGGCCACACGGAGCAGCTCCAGATGTGCAAGTCCGAATCAC
GGACCGGTGGCGTACCCTCCGGGGTCTTGAGATTGAGCTGCAGTTGCAGCTCAGCATGAAAGCCACATTGGAAGGCCGCA
CTGCAGGAACGCAGGCCTGCGTTGAGGCCCAGCTGGTGCAGATCCAGACTCTGAGCAGCGGTGCCGAAGTCCAGCTGGGC
GATGTGTGTGCTGGCTGCCAGGGGAGGCCTGAGCAG

Alignment

ORF - retro_pabe_820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.12 %
• Parental protein coverage: 64.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GELEVKIRDWYQKQGPGPSR-DYSHYYTT-IQDLRDKILGATIENSRIVLQIDNARLAADDFRTKFETEQ
          GEL.VKIR.W..KQGPGP....YSHY..T.I.DLRDKILG.T.ENSRIVLQ.DN.RLAAD.FRTK.E.EQ
Retrocopy GELKVKIRYWDHKQGPGPPA<NYSHYFKT>IEDLRDKILGVTTENSRIVLQTDNPRLAADHFRTKSEVEQ

Parental  ALRMSVEADINGLRRVLDELTLARTDLEMQIEGLKEELAYLKKNHEEEISTLRGQVGGQVSVEVDSAPGT
          ALR.S.EADI....R..DELT.AR..L...I..L.EEL..L.KNH.EEI.......GGQVSVEVDSAPG.
Retrocopy ALRRSLEADIKACGRAPDELTPARAHLKTHIQDLQEELDHLEKNHNEEIRA----AGGQVSVEVDSAPGF

Parental  DLAKILSDMRSQYEVMAEQNRK-DAEAW-FTSRTEELNREVAGHTEQLQMSRSE-VTDLRRTLQGLEIEL
          .LAKIL....SQY.V.AEQ.RK.DAEAW..TS.TEEL..EVAGHTEQLQM..SE..TD..RTL.GLEIEL
Retrocopy CLAKILGNT*SQYAVLAEQMRK<DAEAW<VTSQTEELSWEVAGHTEQLQMCKSE<ITDRWRTLRGLEIEL

Parental  QSQLSMKAALEDTLAETEARFGAQLAHIQALISGIEAQLGDVRADSERQNQE
          Q.QLSMKA.LE...A.T.A...AQL..IQ.L.SG.E.QLGDV.A........
Retrocopy QLQLSMKATLEGRTAGTQACVEAQLVQIQTLSSGAEVQLGDVCAGCQGRPEQ

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	1.60 RPM
SRP007412_cerebellum	0.00 RPM	3.53 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	27.81 RPM
SRP007412_liver	1.77 RPM	2.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_820 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_820 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_959
Gorilla gorilla	retro_ggor_773
Macaca mulatta	retro_mmul_790

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820 ,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,