RetrogeneDB ID: retro_sscr_173

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:123667053..123667698(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000017352
• Aliases: None
• Description: None

Sequence

>retro_sscr_173
GCTGCCTCCTCTGGGGAGAGCGATGAAGCGGGCAGTGGCTTTGGATCCTGGCTAGATGGACGGTTGGAGGCACTGGGAGT
GGACCAAGCCATTTATGGTGCCTACATCCTGGGGGTCCTGCAGGAGAAAGAGGAAGAAGAGAGGCTGGACGCTCTGCAGG
GTATCCTCTCTGCTTTTCCGGAAGGAGATTACCTCCTGAACATCTGCAAGGAGATTGTGGAATGATGGTTGGAAACTCAG
AATGTTATCACTAAAGTGAAAAAAGAAGATGAGGTCCAGGCCATCGCCACCCTCATTGAGAAGCAGGCGCAGATCGTGGT
GAAGCCCAGGATGGTGTCAGAAGAGGAGAAGCAGAGGAAAGCCGCGCTCCTGGCCCAGTATGCTGACGTGACAGACGAAG
AGGATGAAGCAGATGAGAAGGATGATTCAGGTGCCTCCACGATGAACCTTGGTTCTGACAAATCTCTCTTCCGAAACACC
AATGTGGAAGATGTTCTCAATGCCCAAAAACTGGAGCAGGACTCGCTTCGGGATAAGTCCCAAAGGAAGAAGTAATAGGA
CAAGCTGCAGAGGGAGAGGGACAAACTAGCTAAGCAGGAGCACAAGGAAAAGGAAAAGAAAAGGATACAAAGAGGGGAGC
AAAAG

Alignment

ORF - retro_sscr_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.28 %
• Parental protein coverage: 96.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAASGESEEGGSGFGSWLDGRLEALGVDQAIYGAYILGVLQEEEEEEKLDALQGILSAFLEEDSLLNICK
          AA.SGES.E.GSGFGSWLDGRLEALGVDQAIYGAYILGVLQE.EEEE.LDALQGILSAF.E.D.LLNICK
Retrocopy AASSGESDEAGSGFGSWLDGRLEALGVDQAIYGAYILGVLQEKEEEERLDALQGILSAFPEGDYLLNICK

Parental  EIVERWSETQNVTTKVKKEDEVQAIATLIEKQAQIVVKPRMVSEEEKQRKAALLAQYADVTDEEQWEADE
          EIVE.W.ETQNV.TKVKKEDEVQAIATLIEKQAQIVVKPRMVSEEEKQRKAALLAQYADVTDEE..EADE
Retrocopy EIVE*WLETQNVITKVKKEDEVQAIATLIEKQAQIVVKPRMVSEEEKQRKAALLAQYADVTDEED-EADE

Parental  KDDSGASTMNLGSDKSLFRNTNVEDVLNARKLERDSLRDESQRKKEQDKLQRERDKLAKQERKEKEKKRT
          KDDSGASTMNLGSDKSLFRNTNVEDVLNA.KLE.DSLRD.SQRKK..DKLQRERDKLAKQE.KEKEKKR.
Retrocopy KDDSGASTMNLGSDKSLFRNTNVEDVLNAQKLEQDSLRDKSQRKK**DKLQRERDKLAKQEHKEKEKKRI

Parental  QRGERK
          QRGE.K
Retrocopy QRGEQK

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	0.53 RPM	2.79 RPM
SRP014902_testis	0.28 RPM	8.49 RPM
SRP018288_heart	0.31 RPM	10.50 RPM
SRP018288_kidney	0.89 RPM	11.33 RPM
SRP018288_liver	0.48 RPM	4.80 RPM
SRP018288_lung	0.00 RPM	11.10 RPM
SRP018856_adipose	0.97 RPM	11.05 RPM
SRP035408_brain	1.21 RPM	21.50 RPM
SRP035408_liver	0.47 RPM	12.27 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_173 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018379	1 retrocopy	retro_amel_1479,
Canis familiaris	ENSCAFG00000014115	1 retrocopy	retro_cfam_456,
Monodelphis domestica	ENSMODG00000011411	1 retrocopy	retro_mdom_1378,
Mustela putorius furo	ENSMPUG00000009224	1 retrocopy	retro_mputfur_1511,
Oryctolagus cuniculus	ENSOCUG00000017526	1 retrocopy	retro_ocun_1500,
Ochotona princeps	ENSOPRG00000006793	2 retrocopies	retro_opri_263, retro_opri_699,
Rattus norvegicus	ENSRNOG00000002748	1 retrocopy	retro_rnor_2906,
Sus scrofa	ENSSSCG00000017352	2 retrocopies	retro_sscr_173 , retro_sscr_944,