RetrogeneDB ID: retro_ecab_549

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:22675412..22675705(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3S2
• Ensembl ID: ENSECAG00000024044
• Aliases: None
• Description: adaptor-related protein complex 3, sigma 2 subunit [Source:HGNC Symbol;Acc:571]

Sequence

>retro_ecab_549
ATAATCAAGGCAATCCTCACTTTCAACAACCATGGGAAGCATCAGCTCTTCAAGTTCTACTAACCTTACAGTGAAGACAC
AACAGCAGATTATCAGGGAGACTTTCCATTTGGCATTTAAGAGAGATGAAATGTTTGTAATTCCCCAGAAGGAGGATTAC
TAATTGGAGGATCTGACAACAAACTGACTTATAGACATTACACACCGTTATATTTTGTCTTCTGTGTGCATTCTTCAGAG
AGTGAACTTGGCATTTTAAATCTAATTTGAGTATTCCTGGAACATTAGACAAG

Alignment

ORF - retro_ecab_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.65 %
• Parental protein coverage: 50.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MIQAILVFNNHGKPRLVRFYQRFPEEI-QQQIVRETFHLVLKRDD-NICNFLEGGSLIGGSDYKLIYRHY
          .I.AIL.FNNHGK..L..FY....E...QQ.I.RETFHL..KRD..N.CN..EGG.LIGGSD.KL.YRHY
Retrocopy IIKAILTFNNHGKHQLFKFY*PYSEDT>QQ-IIRETFHLAFKRDE<NVCNSPEGGLLIGGSDNKLTYRHY

Parental  ATLYFVFCVDSSESELGILDLIQVFVE-TLDK
          ..LYFVFCV.SSESELGIL.LI.VF.E.TLDK
Retrocopy TPLYFVFCVHSSESELGILNLI*VFLE<TLDK

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	3.25 RPM
SRP021940_cerebellum	0.10 RPM	8.05 RPM
SRP021940_embryo	0.00 RPM	6.09 RPM
SRP021940_placental_villous	0.00 RPM	4.33 RPM
SRP021940_synovial_membrane	0.00 RPM	4.89 RPM
SRP021940_testis	0.00 RPM	9.14 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_549 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_549 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3563
Pan troglodytes	retro_ptro_2420
Macaca mulatta	retro_mmul_1821

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001407	1 retrocopy	retro_btau_436,
Choloepus hoffmanni	ENSCHOG00000003359	4 retrocopies	retro_chof_1775, retro_chof_194, retro_chof_434, retro_chof_88,
Dipodomys ordii	ENSDORG00000004247	1 retrocopy	retro_dord_115,
Equus caballus	ENSECAG00000024044	1 retrocopy	retro_ecab_549 ,
Felis catus	ENSFCAG00000028122	1 retrocopy	retro_fcat_311,
Macropus eugenii	ENSMEUG00000003421	1 retrocopy	retro_meug_2032,
Monodelphis domestica	ENSMODG00000019522	1 retrocopy	retro_mdom_316,
Nomascus leucogenys	ENSNLEG00000011780	2 retrocopies	retro_nleu_1380, retro_nleu_1555,
Otolemur garnettii	ENSOGAG00000030982	1 retrocopy	retro_ogar_1737,
Rattus norvegicus	ENSRNOG00000043141	1 retrocopy	retro_rnor_931,
Sus scrofa	ENSSSCG00000030174	7 retrocopies	retro_sscr_1109, retro_sscr_199, retro_sscr_268, retro_sscr_339, retro_sscr_620, retro_sscr_721, retro_sscr_753,
Tursiops truncatus	ENSTTRG00000015554	2 retrocopies	retro_ttru_1233, retro_ttru_1361,
Vicugna pacos	ENSVPAG00000008668	1 retrocopy	retro_vpac_54,