RetrogeneDB ID: retro_ecab_261

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:16868602..16869001(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000013417
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDFIP1
• Ensembl ID: ENSECAG00000021907
• Aliases: None
• Description: Nedd4 family interacting protein 1 [Source:HGNC Symbol;Acc:17592]

Sequence

>retro_ecab_261
GAGGAAGAGCCCAGGGAAACTGAACAGGCCACAGATGCTGCTCCTCCACCTTATAGCAGCATCTCTGCAGAGTACAGCAT
ATTTTGACTACAAAGATGAGTCTGAATTTCCAAAGCCTCCATCTTATAATGTGGCTACAACACTGTCCAGTTTTGATGAA
GCCGAGAGAACCACGGCTGAAGCTGCCATACCTTTGGTTCCTGGAAGAGATGAGGATTTTGTGGGTCAGGCTGATTTTGA
TGATGCTGACCAAATGAACATAGGAAATGATGAGATTTTTCTTGTTAACTTTTTTTCATGGCATTCCTCTTTAACTGGAT
CAGGTTTTTCGTGTCTTTTTGCCTAACCACCTCAGCTGCAGGAAGGTATGGAGCCATTTCAGAATTTGGTCTCTTTCTA

Alignment

ORF - retro_ecab_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.94 %
• Parental protein coverage: 66.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEEPGEPEQAAGDAPPPYSS-ISAESAAYFDYKDESGFPKPPSYNVATTLPTYDEAERTKAEATIPLVPG
          EEEP.E.EQA..DA.PP..S..S..S.AYFDYKDES.FPKPPSYNVATTL...DEAERT.AEA.IPLVPG
Retrocopy EEEPRETEQAT-DAAPPPYS>ASLQSTAYFDYKDESEFPKPPSYNVATTLSSFDEAERTTAEAAIPLVPG

Parental  RDEDFVGRDDFDDADQLRIGNDGIF-MLTFF-MAFLFNWIGFFLSFCLTTSAAGRYGAISGFGLSL
          RDEDFVG..DFDDADQ..IGND.IF..LTFF.MAFLFNWI.FF.SFCLTTSAAGRYGAIS.FGL.L
Retrocopy RDEDFVGQADFDDADQMNIGNDEIF>LLTFF>MAFLFNWIRFFVSFCLTTSAAGRYGAISEFGLFL

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	95.69 RPM
SRP021940_cerebellum	0.00 RPM	160.52 RPM
SRP021940_embryo	0.03 RPM	50.92 RPM
SRP021940_placental_villous	0.05 RPM	144.57 RPM
SRP021940_synovial_membrane	0.03 RPM	103.88 RPM
SRP021940_testis	0.00 RPM	49.81 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_261 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_261 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047747	1 retrocopy	retro_btau_766,
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175,
Equus caballus	ENSECAG00000021907	1 retrocopy	retro_ecab_261 ,
Homo sapiens	ENSG00000131507	1 retrocopy	retro_hsap_1091,
Gorilla gorilla	ENSGGOG00000004879	1 retrocopy	retro_ggor_859,
Macaca mulatta	ENSMMUG00000016787	1 retrocopy	retro_mmul_846,
Pongo abelii	ENSPPYG00000015896	1 retrocopy	retro_pabe_908,
Pan troglodytes	ENSPTRG00000017358	1 retrocopy	retro_ptro_743,
Sarcophilus harrisii	ENSSHAG00000002466	1 retrocopy	retro_shar_738,
Sus scrofa	ENSSSCG00000025295	1 retrocopy	retro_sscr_301,
Ictidomys tridecemlineatus	ENSSTOG00000005153	1 retrocopy	retro_itri_1454,