RetrogeneDB ID: retro_ecab_970

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:36374103..36374504(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2A
• Ensembl ID: ENSECAG00000012124
• Aliases: None
• Description: RAB2A, member RAS oncogene family [Source:HGNC Symbol;Acc:9763]

Sequence

>retro_ecab_970
GGTAGAGGAAAAGTTTTCCTCCCCAACAATATTACAAGCAGAAATACATTTAACCACTTGACAACCTGGTTAAAAGATGC
CCCCCAGCATTCAAATTCCAACATGGTCATTATGCTTATGGGAAATAAAAGTGATTTAGAATCTAGGAGAGAAGTAAAAA
AAACAAGGTAGAGTCTTTGCATGGTAACACAGACTTATTTCTTCATGGAAACTTGTGCTAAGACTGCTCCCAATATAGAA
GTGGCATTTATTAATACAGCAAAAGAAATTTATGGAAAAGTCCAAGAAGTCTTTGACATTAATAACAAGGAAAATGGCAT
TAAAATGGGCCATCAGCATGCTGCTACTAATGCCACACATGCAGGCTGTCAGGCAGGACAGCAGGCCTGGGAGGTTGCTG
T

Alignment

ORF - retro_ecab_970 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.65 %
• Parental protein coverage: 68.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAAGALLVYDITRRDTFNHLTTWLEDARQHSNSNMVIMLIGNKSDLESRREVKKEEGEAFAREHGLIFME
          G.....L...IT.R.TFNHLTTWL.DA.QHSNSNMVIML.GNKSDLESRRE................FME
Retrocopy GRGKVFLPNNITSRNTFNHLTTWLKDAPQHSNSNMVIMLMGNKSDLESRREXXXXR*SLCMVTQTYFFME

Parental  TSAKTASNVEEAFINTAKEIYEKIQEGVFDINNEANGIKIGPQHAATNATHAGNQGGQQAG-GGCC
          T.AKTA.N.E.AFINTAKEIY.K.QE.VFDINN..NGIK.G.QHAATNATHAG.Q.GQQA..GGCC
Retrocopy TCAKTAPNIEVAFINTAKEIYGKVQE-VFDINNKENGIKMGHQHAATNATHAGCQAGQQAW<GGCC

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	49.11 RPM
SRP021940_cerebellum	0.00 RPM	127.75 RPM
SRP021940_embryo	0.00 RPM	47.05 RPM
SRP021940_placental_villous	0.00 RPM	76.98 RPM
SRP021940_synovial_membrane	0.00 RPM	51.55 RPM
SRP021940_testis	0.00 RPM	59.85 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_970 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_970 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_970 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007153	1 retrocopy	retro_cfam_2057,
Equus caballus	ENSECAG00000012124	1 retrocopy	retro_ecab_970 ,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Sorex araneus	ENSSARG00000013511	2 retrocopies	retro_sara_688, retro_sara_744,
Tarsius syrichta	ENSTSYG00000013060	1 retrocopy	retro_tsyr_1215,
Tursiops truncatus	ENSTTRG00000009615	1 retrocopy	retro_ttru_1377,