RetrogeneDB ID: retro_ecab_650

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 25:32715624..32716290(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT7
• Ensembl ID: ENSECAG00000022693
• Aliases: None
• Description: septin 7 [Source:HGNC Symbol;Acc:1717]

Sequence

>retro_ecab_650
CAACAACTGAAAGAAACCCAAGAATATAAAATTAAAATAGATGAACTTCCAGCAACAGATGATGAAGAAGAAAAGCTTGT
TAAAAACATAAAGGACCATTCACCTCTTGCTGTGAACGGTAGTAACTTCATTGAAGTTAGCGGCAGAAGGGTCAGAGGAA
GGCCGCATCCTTGGGGTGTTGCTGACATTGAAAATGGTGAAGATTGTGATTTTACAATTCTAAGAAATATGTTAATACGA
GGACACTTGCAGGACTTGTAAGATGTCACTAATAATGTACGCTATGAGAACTACAGAGGCAGAAAACTGACAGCTGTGAC
GTCCGTTGGAGTTGATAACAGCGAGAACAAAGGGCAGCTTCTGAAGAGCCCTCGGGCACCCATGGAAGAAGAAGGAAGAG
ACATGGTGGCCACGATGAGGGAGATGGAGATGGAGCAGGTGTTTGAGACGAAGGCCAGAGAAGAAGTTCAAAACTGAAGG
ATTCTGAGGGCAAGCACCAACGGCACCATGAGTAAACAAAAAAGAATTTGGAAGCAGCGCAAGGAATTAGAGGACGAATG
TCGCCAGTTTGAAGATGAGAAGGCAAACTGGGAAGCTGAGCGGATTTTAGAACAACCGAGCTCTCTGAGAAGCTTGGAAA
AGAACAAGAAGGAGGCAAAGGTCTTT

Alignment

ORF - retro_ecab_650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 54.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QIMKEIQEHKIKIYEFPETDDEEENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEH
          Q..KE.QE.KIKI.E.P.TDDEEE.KLVK.IKD..PLAV.GSN..IEV.G.RVRGR..PWGVA..ENGE.
Retrocopy QQLKETQEYKIKIDELPATDDEEE-KLVKNIKDHSPLAVNGSN-FIEVSGRRVRGRPHPWGVADIENGED

Parental  CDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKSPLAQMEEERREHVAK
          CDFTILRNMLIR.H.QDL.DVTNNV.YENYR.RKL.AVT..GVDN..NKGQL.KSP.A.MEEE.R..VA.
Retrocopy CDFTILRNMLIRGHLQDL*DVTNNVRYENYRGRKLTAVTSVGVDNSENKGQLLKSPRAPMEEEGRDMVAT

Parental  MKKMEMEMEQVFEMKVKEKVQ-KLKDSEAELQRRHEQ-MKKNLEAQHKELEEKRRQFEDEKANWEAQQRI
          M...EMEMEQVFE.K..E.VQ.KLKDSE...QR.H.....K....Q.KELE...RQFEDEKANWEA..RI
Retrocopy MR--EMEMEQVFETKAREEVQ<KLKDSEGKHQR-HHE>KQKRIWKQRKELEDECRQFEDEKANWEA-ERI

Parental  LEQQNSSRTLEKNKKKGKIF
          LEQ..S.R.LEKNKK..K.F
Retrocopy LEQPSSLRSLEKNKKEAKVF

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	47.58 RPM
SRP021940_cerebellum	0.05 RPM	23.32 RPM
SRP021940_embryo	0.05 RPM	110.40 RPM
SRP021940_placental_villous	0.05 RPM	52.68 RPM
SRP021940_synovial_membrane	0.03 RPM	41.81 RPM
SRP021940_testis	0.00 RPM	10.23 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_650 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_650 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Equus caballus	ENSECAG00000022693	1 retrocopy	retro_ecab_650 ,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258,
Tursiops truncatus	ENSTTRG00000016197	1 retrocopy	retro_ttru_329,