RetrogeneDB ID: retro_ecab_211

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:16468659..16468958(+)
• Located in intron of: ENSECAG00000026972

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBAG9
• Ensembl ID: ENSECAG00000009719
• Aliases: None
• Description: estrogen receptor binding site associated, antigen, 9 [Source:HGNC Symbol;Acc:3123]

Sequence

>retro_ecab_211
CAGAAAATCAGTATTGAGAAGAGTGAACCATTAAATTTTCACTAGTCAATTGGTAGCACAGATTCTCTAGTAAATTAGCA
GCTACATGAGATATTCTTTTTATGCATCCATCTCCAGAATTAGGTGACAGATGCACCCGGCAAGAAAATACCAATGCACG
GGAAGAAGGTGTGGCCTGGCGAGCAGAAGTTCTGTAGCAGCAGAAAGTAGCAGATGGAGAACAGAGAGCAGCAAAAAACA
GAAGAAAATGGAAAAGGAAGCTCAGGAGGAAGGAAAAAGGAACAATCGAAACTGACCTG

Alignment

ORF - retro_ecab_211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.48 %
• Parental protein coverage: 50.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKIIIKKREPLNFGIPDGSTG-FSSRLAATQDMPFIHQSPELGDLDTWQENTNAWEEEEDAAWQAEEVLR
          QKI.I.K.EPLNF....GST..FSS.LAAT.D..F.H.SPELGD..T.QENTNA...EE..AW.A.EVL.
Retrocopy QKISIEKSEPLNFH*SIGSTD<FSSKLAAT*DILFMHPSPELGDRCTRQENTNA--REEGVAWRA-EVL*

Parental  QQKIADREKRAAEQQRKKMEKEAQRLMKKEQNKIGVKL
          QQK.AD.E.RAA...RK...K....L..KE...I...L
Retrocopy QQKVADGEQRAAKNRRKWKRK----LRRKEKGTIETDL

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	24.03 RPM
SRP021940_cerebellum	0.26 RPM	18.54 RPM
SRP021940_embryo	0.13 RPM	15.83 RPM
SRP021940_placental_villous	0.00 RPM	16.31 RPM
SRP021940_synovial_membrane	0.00 RPM	8.48 RPM
SRP021940_testis	0.00 RPM	25.90 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_211 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_211 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211 , retro_ecab_232,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,