RetrogeneDB ID: retro_sscr_1117

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: GL895718.2:29679..30044(+)
• Located in intron of: ENSSSCG00000030641

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000010353
• Aliases: None
• Description: None

Sequence

>retro_sscr_1117
GGAGAGGTTTCAACAATGACCAGGAGTGGGATCTGCATGGCAGGGAGCATTGAGGAAGCAGGCTGGAGAAATTAGTGGGA
AAGCTGGTACCTGCCTGGCTGGGCAACCCCTCCTACCTTCCCACCTTCCTGGGCACCTACAGAGCTTCTGCCACCAACCA
GCAGGTGCTGGGCCTTCTGTTCCAAAGGTACAGCTGCACCCTCCCTTATTCTGATGAGGACTGGGGGGGGGGGGGCTCCC
TGCACCAGCTCAGAATGGCCATGCCCTCCATCCTGGGCACCTGGCTGAACCAGCATCCTGAGGACTTCCGCCAGCCCCCA
GAAATTCCCTGCCTAAAGATGCTCTTGTCTTACCCAGAGTGCTCA

Alignment

ORF - retro_sscr_1117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 53.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSVDQSLRRGTCMVGSIQ-GNRLDKLVAQLVPALLGGDRSFLLTFLGTYTASATTQQVLDLLFLRYGCIL
          G.V....R.G.CM.GSI..G.RL.KLV..LVPA.LG...S.L.TFLGTY.ASAT.QQVL.LLF.RY.C.L
Retrocopy GEVSTMTRSGICMAGSIE<GSRLEKLVGKLVPAWLGNP-SYLPTFLGTYRASATNQQVLGLLFQRYSCTL

Parental  PYAEEDGGP---LHQLRMAMTSILGTWLDQYPEDFHQPPEFPCLKMLLAYLELS
          PY..ED......LHQLRMAM.SILGTWL.Q.PEDF.QPPE.PCLKMLL.Y.E.S
Retrocopy PYSDEDXXXXXSLHQLRMAMPSILGTWLNQHPEDFRQPPEIPCLKMLLSYPECS

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	0.13 RPM	0.00 RPM
SRP014902_testis	0.14 RPM	0.00 RPM
SRP018288_heart	0.21 RPM	0.00 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.16 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.15 RPM	0.00 RPM
SRP035408_brain	0.10 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1117 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1117 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000033014	2 retrocopies	retro_rnor_1368, retro_rnor_1369,
Sus scrofa	ENSSSCG00000010353	1 retrocopy	retro_sscr_1117 ,