RetrogeneDB ID: retro_ecab_534

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:7520153..7520675(+)
• Located in intron of: ENSECAG00000009007

Retrocopy information

• Ensembl ID: ENSECAG00000014177
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YRDC
• Ensembl ID: ENSECAG00000022522
• Aliases: None
• Description: yrdC domain containing (E. coli) [Source:HGNC Symbol;Acc:28905]

Sequence

>retro_ecab_534
GTGTACTGCCTCAAGGGCCGCAGCGAGGCCAAGCTGCTAGCCGTATGCCTGGGCCTTGTGGCCGACATCTACAGGTACTG
CCATGTGAGAGCACCCGAGGGGCTCCTGAAAGACCTGTTACCAGTACCAATGACCCTGGTGATGGAACGCTCAGAGCAGC
TCAACAAGGACCTGAACCCCTTCACTCCTCTTGTAGGCATCCGGATTCCTGACCATGCCTTCATGCAGGACTTGGCCCGG
GTGTTTGGGGGACCACTTCCCCTCACCAGCGCTCACCTCAGCTCCCAGGCCAGTTCTCTGAATGTCGAGGAGTTCCAGGA
CCTCTGGCCTCAGTTGTCCCTGGTCATTGATGGGGAACCAGCTGGGGATGGCCAGAGCTCTGAGTATCACCTAGGCTCAG
CTGTGGTTGACGTGTCTGTGCCTGGAAGGTTTGGCATCATTTGTCCAGGCTGTGCCCTGGAAAGTACTACAGCCATCCTC
CAACAGAAGTACAGGCTGCTCCCTTCGTACAGATCCTGCTTG

Alignment

ORF - retro_ecab_534 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.91 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYRLKSRSEPAC-AVCLGRVADVYRYCHVRVPEGLLKDLLPGPVTLVMERSEELNKDLNPFTPLVGIRIP
          VY.LK.RSE....AVCLG.VAD.YRYCHVR.PEGLLKDLLP.P.TLVMERSE.LNKDLNPFTPLVGIRIP
Retrocopy VYCLKGRSEAKLLAVCLGLVADIYRYCHVRAPEGLLKDLLPVPMTLVMERSEQLNKDLNPFTPLVGIRIP

Parental  DHAFMQDLAQVFGGPLALTSANLSSQASSLNVEEFQDLWPQLSLVVDGGPIGDGQSPECRLGSTVVDLSV
          DHAFMQDLA.VFGGPL.LTSA.LSSQASSLNVEEFQDLWPQLSLV.DG.P.GDGQS.E..LGS.VVD.SV
Retrocopy DHAFMQDLARVFGGPLPLTSAHLSSQASSLNVEEFQDLWPQLSLVIDGEPAGDGQSSEYHLGSAVVDVSV

Parental  PGKFGIIRPGCALESTTAILQQKYGLLPSHGSCL
          PG.FGII.PGCALESTTAILQQKY.LLPS..SCL
Retrocopy PGRFGIICPGCALESTTAILQQKYRLLPSYRSCL

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	0.24 RPM	3.60 RPM
SRP021940_cerebellum	0.10 RPM	10.91 RPM
SRP021940_embryo	0.23 RPM	4.50 RPM
SRP021940_placental_villous	0.24 RPM	4.86 RPM
SRP021940_synovial_membrane	0.05 RPM	4.28 RPM
SRP021940_testis	0.00 RPM	9.40 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_534 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_534 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001173	1 retrocopy	retro_amel_350,
Dasypus novemcinctus	ENSDNOG00000009111	2 retrocopies	retro_dnov_1774, retro_dnov_2232,
Equus caballus	ENSECAG00000022522	1 retrocopy	retro_ecab_534 ,
Felis catus	ENSFCAG00000011018	1 retrocopy	retro_fcat_375,
Homo sapiens	ENSG00000196449	2 retrocopies	retro_hsap_4199, retro_hsap_4289,
Gorilla gorilla	ENSGGOG00000007619	1 retrocopy	retro_ggor_2866,
Macropus eugenii	ENSMEUG00000005068	1 retrocopy	retro_meug_452,
Microcebus murinus	ENSMICG00000011953	1 retrocopy	retro_mmur_188,
Myotis lucifugus	ENSMLUG00000000955	1 retrocopy	retro_mluc_367,
Macaca mulatta	ENSMMUG00000005372	2 retrocopies	retro_mmul_1206, retro_mmul_1662,
Nomascus leucogenys	ENSNLEG00000011665	2 retrocopies	retro_nleu_1045, retro_nleu_1046,
Otolemur garnettii	ENSOGAG00000030474	2 retrocopies	retro_ogar_1107, retro_ogar_2342,
Pongo abelii	ENSPPYG00000001523	1 retrocopy	retro_pabe_3495,
Pan troglodytes	ENSPTRG00000000557	4 retrocopies	retro_ptro_2850, retro_ptro_2906, retro_ptro_2907, retro_ptro_2999,
Tupaia belangeri	ENSTBEG00000008863	1 retrocopy	retro_tbel_1817,
Tarsius syrichta	ENSTSYG00000005555	3 retrocopies	retro_tsyr_1108, retro_tsyr_1420, retro_tsyr_874,