RetrogeneDB ID: retro_ecab_401

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:65270341..65270807(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSECAG00000019946
• Aliases: None
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_ecab_401
ATTGAAGTGCATTTGCTTATTCAGCTAAAGCCATGGGAAGATACAAGGATGGATTTACCATTATTCCTGAACTGGGTAGA
GTTCAGGGTGAATCAAAAGAGTAGAATTTGGTGAGACTCTTCAGTAAATCTCTGGAGATCCTAATAATCTCTTTGGGATT
TCTTCTGATATCTACCACTGGGGTCAAACGTTCCTTACAGTTATAAGCGTGAAACCTAGGGGGAGAGTTATAGATTCATT
GGACATCTAGGTAAAATGGATAATGATATTATGGAAGAATTAGGCTCTGTATCTTTTAGCACTTACTTAGAAACATACCA
AATATAACTTGTGGAAGACATCCCATTAGGATGTTATTAAATGTTACGGAGTTCTAGAAGAATGGGATGAATATGAGCTT
CACTTTCTTGAATTATGCCAGGCAAGTCCATGTAGAAACTGGCAAGACAGTTCTGTAAGTTGTGCT

Alignment

ORF - retro_ecab_401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.35 %
• Parental protein coverage: 57.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IEMHL-PYTAKAMESHKDEFTIIPVLVGALSESKEQEFGKLFSKYL-ADPSNLFVVSSDFCHWGQRF-RY
          IE.HL..Y.AKAM...KD.FTIIP.L.....ESKE.....LFSK.L..DP.NLF..SSD..HWGQ.F..Y
Retrocopy IEVHL<AYSAKAMGRYKDGFTIIPELGRVQGESKE*NLVRLFSKSL<GDPNNLFGISSDIYHWGQTF<PY

Parental  SYYDESQGEIYRSIEHLDKMGMSIIEQLDPVSFSNYLKKYH-NTICGRHPIGVLLNAITELQKNGMNMSF
          SY..E..GE.YR.I.HL.KM...I.E.L..VSFS.YL..Y..N..CGRHPI..LLN..TE..KNGMNMSF
Retrocopy SYKRET*GESYRFIGHLGKMDNDIMEELGSVSFSTYLETYQ<NITCGRHPIRMLLN-VTEF*KNGMNMSF

Parental  SFLNYA-QSSQCRNWQDSSVSYA
          .FLNYA.Q.S.CRNWQDSSVS.A
Retrocopy TFLNYA<QASPCRNWQDSSVSCA

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	1.95 RPM
SRP021940_cerebellum	0.00 RPM	7.48 RPM
SRP021940_embryo	0.00 RPM	10.89 RPM
SRP021940_placental_villous	0.00 RPM	11.21 RPM
SRP021940_synovial_membrane	0.00 RPM	9.03 RPM
SRP021940_testis	0.00 RPM	128.97 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_401 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_401 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_401 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007771	1 retrocopy	retro_amel_1500,
Equus caballus	ENSECAG00000019946	1 retrocopy	retro_ecab_401 ,
Echinops telfairi	ENSETEG00000007994	1 retrocopy	retro_etel_561,
Felis catus	ENSFCAG00000001385	1 retrocopy	retro_fcat_642,
Homo sapiens	ENSG00000162959	2 retrocopies	retro_hsap_2507, retro_hsap_3522,
Myotis lucifugus	ENSMLUG00000016108	1 retrocopy	retro_mluc_1923,
Mus musculus	ENSMUSG00000058704	1 retrocopy	retro_mmus_834,
Nomascus leucogenys	ENSNLEG00000015577	1 retrocopy	retro_nleu_488,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Otolemur garnettii	ENSOGAG00000010975	3 retrocopies	retro_ogar_1860, retro_ogar_2049, retro_ogar_3050,
Pongo abelii	ENSPPYG00000012511	1 retrocopy	retro_pabe_2910,