RetrogeneDB ID: retro_ecab_27

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un0007:131391..131979(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000013137
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM168B
• Ensembl ID: ENSECAG00000017018
• Aliases: None
• Description: family with sequence similarity 168, member B [Source:HGNC Symbol;Acc:27016]

Sequence

>retro_ecab_27
ATGAATCCTGTTTATAGCCCTGGTTCTTCTGGGGTTCCCTATGCAAATGCCAAAGGAATTGGTTATCCAGCTGGTTTCCC
CATGGGCTACGCAGCAGCGGCTCCCACCTACTCCCCCAACATGTACCCTGGAGCGAACCCCACCTTCCAAACAGGTTACA
CTCCTGGCACACCTTACAAAGTGTCCTGTTCCCCCACCAGTGGGGCAGTGCCACCATACTCCTCCTCCCCCAACCCCTAC
CAGACCGCCGTGTACCCCGTGCGAAGTGCCTACCCCCAGCAGAGCCCATACGCACAGCAAGGCACATACTGCACACAACC
CCTGTACGCAGCACCTCCTCACGTCGTCCACCACACCACGGTGGTGCAACCCAATGGCATGCCGATGACGGTGTACCCTG
CACCTATCCCTCCACCTACAGGCAACGGGGTCACCATGGGCATGGTGGCTGGGACCACTATGGCGATGTCAGCAGGTACC
CTGCTGACTGCCCACTCCCCAACTCCTGTCGCCCCTCACCGAGTCAAGGTGCCCACATATCCGGCCCCCGGAACACCCAC
CTACAGCTACGTGCCCCCTCCGTGGTGA

Alignment

ORF - retro_ecab_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.38 %
• Parental protein coverage: 97.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPVYSPGSSGVPYANAKGIGYPAGFPMGYAAAAPAYSPNMYPGANPTFQTGYTPGTPYKVSCSPTSGAV
          MNPVYSPGSSGVPYANAKGIGYPAGFPMGYAAAAP.YSPNMYPGANPTFQTGYTPGTPYKVSCSPTSGAV
Retrocopy MNPVYSPGSSGVPYANAKGIGYPAGFPMGYAAAAPTYSPNMYPGANPTFQTGYTPGTPYKVSCSPTSGAV

Parental  PPYSSSPNPYQTAVYPVRSAYPQQSPYAQQGTYYTQPLYAAPPHVIHHTTVVQPNGMPATVYPAPIPPPR
          PPYSSSPNPYQTAVYPVRSAYPQQSPYAQQGTY.TQPLYAAPPHV.HHTTVVQPNGMP.TVYPAPIPPP.
Retrocopy PPYSSSPNPYQTAVYPVRSAYPQQSPYAQQGTYCTQPLYAAPPHVVHHTTVVQPNGMPMTVYPAPIPPPT

Parental  GNGVTMGMVAGTTMAMSAGTLLTAHSPTPVAPHPVTVPTYRAPGTPTYSYVPPQW
          GNGVTMGMVAGTTMAMSAGTLLTAHSPTPVAPH.V.VPTY.APGTPTYSYVPP.W
Retrocopy GNGVTMGMVAGTTMAMSAGTLLTAHSPTPVAPHRVKVPTYPAPGTPTYSYVPPPW

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	10.09 RPM
SRP021940_cerebellum	0.00 RPM	27.58 RPM
SRP021940_embryo	0.03 RPM	31.25 RPM
SRP021940_placental_villous	0.00 RPM	14.96 RPM
SRP021940_synovial_membrane	0.00 RPM	20.34 RPM
SRP021940_testis	0.00 RPM	20.53 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_27 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_27 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_27 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004222	2 retrocopies	retro_cfam_1748, retro_cfam_344,
Choloepus hoffmanni	ENSCHOG00000009590	1 retrocopy	retro_chof_551,
Equus caballus	ENSECAG00000017018	1 retrocopy	retro_ecab_27 ,
Felis catus	ENSFCAG00000000303	1 retrocopy	retro_fcat_1218,
Monodelphis domestica	ENSMODG00000018633	1 retrocopy	retro_mdom_1625,
Mustela putorius furo	ENSMPUG00000011824	1 retrocopy	retro_mputfur_454,
Ictidomys tridecemlineatus	ENSSTOG00000000206	2 retrocopies	retro_itri_191, retro_itri_262,
Tupaia belangeri	ENSTBEG00000017162	1 retrocopy	retro_tbel_83,