RetrogeneDB ID: retro_ecab_408

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:17151251..17151746(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX3
• Ensembl ID: ENSECAG00000017026
• Aliases: None
• Description: peroxiredoxin 3 [Source:HGNC Symbol;Acc:9354]

Sequence

>retro_ecab_408
TTGACAAACATATAGTGATCTTGTTCTGGTCAAGCAAAATTTACCTTTAGCACCAGTTCCTCAGATCATGCTCCTGCTGT
CAGCCAGTGTGGACCCTCTTTTAGTGGAATAGCTGATGTCAATGGAGAATTCAAAGAACTAAGCTTTCATGACTTTAAGG
GGAAATATTTGGTGCTTTTCTTTTATCCTTTGGATTTCACCTTTATGTGTCCTACAGAAATTGTTGCCTTTGGTGATTAA
GCCAATGAGTTTCATGATGTGAACTGTGAAGTTGTTGTAGTTTTGGTGAGTTCTTTCTTTGCCATCTTGACTGATAAATA
TACAAAGGAAGAAAGGCAGTTTGGGCCACAAGAACATTGCAGTCTTGTCAGATCTGACTAAACAAAAATTTCCTGAGACT
ACAGTGTGCTGTCCCTGAGAGGTCTTGCACTAAGAGGTCTCTTCATGACTGACCCCAGTGGAGATATGAAGCATTCGAGT
ATGAATATCCTCCCA

Alignment

ORF - retro_ecab_408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.69 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTNVLWSGFNQAKLAFSTSSSYHTPAVTQHAPYFKGTAVVKGEFKELSLDDFKGKYLVLFFYPLDFTFVC
          LTN...S...QAK..FSTSSS.H.PAV.Q..P.F.G.A.V.GEFKELS..DFKGKYLVLFFYPLDFTF.C
Retrocopy LTNI**SCSGQAKFTFSTSSSDHAPAVSQCGPSFSGIADVNGEFKELSFHDFKGKYLVLFFYPLDFTFMC

Parental  PTEIVAFSDKANEFHDVNCEVVAVSVDSHFSHLAW-INTPRKNGGLGHMNIPLLSDLTKQISRDYGV-LL
          PTEIVAF.D.ANEFHDVNCE.V.V...S.F......IN..RK.G.LGH.NI..LSDLTKQ......V..L
Retrocopy PTEIVAFGD*ANEFHDVNCE-VVVVLVSSFFAILT>INIQRKKGSLGHKNIAVLSDLTKQKFPETTV<VL

Parental  EGAGLALRGLFIIDPNGVIKHLSVNDLP
          ...GLALRGLF..DP.G..KH.S.N.LP
Retrocopy SLRGLALRGLFMTDPSGDMKHSSMNILP

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
SRP021940_articular_cartilage	0.00 RPM	9.03 RPM
SRP021940_cerebellum	0.00 RPM	41.91 RPM
SRP021940_embryo	0.00 RPM	33.04 RPM
SRP021940_placental_villous	0.00 RPM	22.32 RPM
SRP021940_synovial_membrane	0.00 RPM	15.62 RPM
SRP021940_testis	0.00 RPM	28.45 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_408 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_408 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus	ENSCJAG00000019636	3 retrocopies	retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi	ENSCSAVG00000001209	1 retrocopy	retro_csav_6,
Dasypus novemcinctus	ENSDNOG00000001359	3 retrocopies	retro_dnov_1052, retro_dnov_2373, retro_dnov_745,
Equus caballus	ENSECAG00000008678	1 retrocopy	retro_ecab_81,
Equus caballus	ENSECAG00000010085	1 retrocopy	retro_ecab_576,
Equus caballus	ENSECAG00000017026	1 retrocopy	retro_ecab_408 ,
Erinaceus europaeus	ENSEEUG00000009299	1 retrocopy	retro_eeur_238,
Homo sapiens	ENSG00000165672	3 retrocopies	retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Macropus eugenii	ENSMEUG00000007732	3 retrocopies	retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus	ENSMICG00000007627	1 retrocopy	retro_mmur_475,
Myotis lucifugus	ENSMLUG00000012871	3 retrocopies	retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica	ENSMODG00000009286	1 retrocopy	retro_mdom_1062,
Mustela putorius furo	ENSMPUG00000003074	1 retrocopy	retro_mputfur_1032,
Nomascus leucogenys	ENSNLEG00000016698	3 retrocopies	retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus	ENSOCUG00000017334	2 retrocopies	retro_ocun_135, retro_ocun_1434,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29,
Ictidomys tridecemlineatus	ENSSTOG00000002537	2 retrocopies	retro_itri_1098, retro_itri_1753,
Tupaia belangeri	ENSTBEG00000011064	5 retrocopies	retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus	ENSTTRG00000010878	2 retrocopies	retro_ttru_1703, retro_ttru_881,