RetrogeneDB ID: retro_sscr_414

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:56646390..56646773(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000025544
• Aliases: None
• Description: None

Sequence

>retro_sscr_414
ATGGGAAACAATTTTCCCAAGATGGATAAACATTTCTTATCAGTACGCATTTGTCGTAACTTCATACTTGATGGAGTTCA
CATAATAGTTGACCATCTGCATGCAGAAGCACCAGATGACTTGCATGAGAAGATGCTTAAAAATTTGTTCTTTATCTCAA
TGCAGGCCAATTAAATGTTTAGAAGAGTTACTCAACAGCAGAGACTTTATGGCAAACTTAGTGGGATATTTCACATTTTG
CCACAAGGCTCTCCAAAGAACATGAGCTAAAATTTCAGAGACTGTCATGAGATTCCTTGAGAAACTATCTGACAAAATAT
TCTGAAGAAACTATAAAAGGTGCTTCGATGGTATGAGAAATAACAATAAAACTAAATCTTCAA

Alignment

ORF - retro_sscr_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.06 %
• Parental protein coverage: 93.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGTNLPVKAEKHLLPERVWHHFEVAGDHVVVDGLRAEAPDDLVR-EAAYKIFLYPNAGQL-KCLEELLSN
          MG.N.P.K..KH.L..R....F...G.H..VD.L.AEAPDDL...E.A.K..LY.NAGQL.KCLEELL..
Retrocopy MGNNFP-KMDKHFLSVRICRNFILDGVHIIVDHLHAEAPDDLHE<EDA*KFVLYLNAGQL<KCLEELLNS

Parental  RDLLAKLVGYESFSHRALQGTMARSPETVMQFLEKLSDKL-SERTMKDFEMMRGMKMKLNPQ
          RD..A.LVGY..F.H.ALQ.T.A...ETVM.FLEKLSDK..SE.T.K...M......KLN.Q
Retrocopy RDFMANLVGYFTFCHKALQRT*AKISETVMRFLEKLSDKI>SEETIKGASMV*EITIKLNLQ

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
SRP014902_placenta	0.00 RPM	3.72 RPM
SRP014902_testis	0.00 RPM	6.51 RPM
SRP018288_heart	0.00 RPM	6.99 RPM
SRP018288_kidney	0.00 RPM	13.50 RPM
SRP018288_liver	0.00 RPM	4.96 RPM
SRP018288_lung	0.00 RPM	2.34 RPM
SRP018856_adipose	0.00 RPM	5.65 RPM
SRP035408_brain	0.00 RPM	3.37 RPM
SRP035408_liver	0.00 RPM	7.57 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_414 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_414 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000027001	1 retrocopy	retro_hsap_3891,
Gorilla gorilla	ENSGGOG00000009424	1 retrocopy	retro_ggor_2619,
Macaca mulatta	ENSMMUG00000006942	1 retrocopy	retro_mmul_1732,
Nomascus leucogenys	ENSNLEG00000013401	1 retrocopy	retro_nleu_1131,
Pongo abelii	ENSPPYG00000005207	1 retrocopy	retro_pabe_3172,
Sus scrofa	ENSSSCG00000025544	1 retrocopy	retro_sscr_414 ,