RetrogeneDB ID: retro_sscr_763

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:113496440..113496747(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000021827
• Aliases: None
• Description: None

Sequence

>retro_sscr_763
ATGGAAAAAAGTCTATGCCTTCTTGAAATAGATGATCCTGAGTTTCATGTCCATGTTTCTGGAGGAAGTATCAAAAAAAT
GCTCTATGACGAAGGCTGTCCTAAAGTATTCCCAATGGCAGCTCTGTCGAAATTTGTTTCAGAAGGAGACAATATCCTAG
ATGCATTAAGACTCATTGAGTATCTTGATGTGTGTCTTCAGATAGTCAAACCCAAGTTGTGATGACCCCACAGCATCTGC
CTTGCAGTGGAAAATGCCAAGTTCTTGGAGACTGCTTTTTGGCCGTGGCCTTACAAATGTAATTTTT

Alignment

ORF - retro_sscr_763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEKSPCIPEIDDSEFCVRVPGGGITKTLYDEGCSKGIPMAVLLKFVSEGDNIPDALGLVEYLNEWLQIIK
          MEKS.C..EIDD.EF.V.V.GG.I.K.LYDEGC.K..PMA.L.KFVSEGDNI.DAL.L.EYL...LQI.K
Retrocopy MEKSLCLLEIDDPEFHVHVSGGSIKKMLYDEGCPKVFPMAALSKFVSEGDNILDALRLIEYLDVCLQIVK

Parental  -PCCEDTTESALPWKMPSSWRLLFGSGLPPALF
          .P.C.D.T.SAL.WKMPSSWRLLFG.GL....F
Retrocopy >PSCDDPTASALQWKMPSSWRLLFGRGLTNVIF

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	2.65 RPM
SRP014902_testis	0.00 RPM	3.39 RPM
SRP018288_heart	0.00 RPM	10.56 RPM
SRP018288_kidney	0.00 RPM	15.47 RPM
SRP018288_liver	0.00 RPM	9.27 RPM
SRP018288_lung	0.00 RPM	8.15 RPM
SRP018856_adipose	0.00 RPM	7.80 RPM
SRP035408_brain	0.00 RPM	11.56 RPM
SRP035408_liver	0.00 RPM	13.15 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_763 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_763 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_763 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018855	1 retrocopy	retro_cfam_424,
Choloepus hoffmanni	ENSCHOG00000010042	1 retrocopy	retro_chof_1738,
Myotis lucifugus	ENSMLUG00000017744	1 retrocopy	retro_mluc_2496,
Macaca mulatta	ENSMMUG00000021855	1 retrocopy	retro_mmul_198,
Nomascus leucogenys	ENSNLEG00000009063	1 retrocopy	retro_nleu_1753,
Oryctolagus cuniculus	ENSOCUG00000005086	1 retrocopy	retro_ocun_1448,
Sus scrofa	ENSSSCG00000021827	2 retrocopies	retro_sscr_1008, retro_sscr_763 ,