RetrogeneDB ID: retro_sscr_184

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:145909858..145910246(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000004770
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL18A
• Ensembl ID: ENSSSCG00000013889
• Aliases: None
• Description: ribosomal protein L18a [Source:HGNC Symbol;Acc:10311]

Sequence

>retro_sscr_184
TACTTGGTGTCTCAGCTGAAGATGAAGACATCAGCAGTGGATATTATCTACTGTGGACAGGTGTTCCAGAAGTATCCCCT
GAGGGTGAAGAACTTCGGCATCTGGCTGTGTTATGATTCCCTTGTTAGCACCCACCAGGAGTACGAGATACCAGGACCTG
ACCACAGCTGGCACCATCACCCAGTGCTACAGAGACATGGTGCTTGGCACCATGCCCAGGGCCCATTCCAGCCAGATCAA
GAAGGTGGAGGAGATTGCAGCCAACAAGTGCCTCCAACCAGCAGTCAAGCAGTTCCAGGACTCCAAGATCAAGTTCCTGC
TTCCCTATCAGGTTTTTTGTCACCTGCACAAGCCATGCTTCACCACCAAGAGCCCAAACACCTTCTTT

Alignment

ORF - retro_sscr_184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 58.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YFVSQLKKMKKSSGEIVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMY-REYR-DLTTAGAVTQCYRDM
          Y.VSQLK.MK.S...I.YCGQVF.K.PLRVKNFGIWL.YDS...TH..Y.R..R.DLTTAG..TQCYRDM
Retrocopy YLVSQLK-MKTSAVDIIYCGQVFQKYPLRVKNFGIWLCYDSLVSTHQEY<RDTR<DLTTAGTITQCYRDM

Parental  GARHRARAHSIQIMKVEEIAASKCRRPAVKQFHDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF
          ......RAHS.QI.KVEEIAA.KC..PAVKQF.DSKIKF.LP..V....HKP.FTTK.PNTFF
Retrocopy VLGTMPRAHSSQIKKVEEIAANKCLQPAVKQFQDSKIKFLLPYQVFCHLHKPCFTTKSPNTFF

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	823.73 RPM
SRP014902_testis	0.00 RPM	606.52 RPM
SRP018288_heart	0.00 RPM	208.61 RPM
SRP018288_kidney	0.00 RPM	229.42 RPM
SRP018288_liver	0.00 RPM	271.05 RPM
SRP018288_lung	0.00 RPM	509.54 RPM
SRP018856_adipose	0.00 RPM	461.17 RPM
SRP035408_brain	0.00 RPM	199.65 RPM
SRP035408_liver	0.00 RPM	149.92 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_184 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_184 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003125	1 retrocopy	retro_acar_86,
Bos taurus	ENSBTAG00000015831	5 retrocopies	retro_btau_145, retro_btau_1586, retro_btau_842, retro_btau_917, retro_btau_922,
Canis familiaris	ENSCAFG00000015122	1 retrocopy	retro_cfam_231,
Callithrix jacchus	ENSCJAG00000014006	7 retrocopies	retro_cjac_1628, retro_cjac_2814, retro_cjac_3192, retro_cjac_3906, retro_cjac_4134, retro_cjac_441, retro_cjac_642,
Cavia porcellus	ENSCPOG00000015205	1 retrocopy	retro_cpor_1478,
Equus caballus	ENSECAG00000015258	1 retrocopy	retro_ecab_745,
Felis catus	ENSFCAG00000007518	6 retrocopies	retro_fcat_1190, retro_fcat_1213, retro_fcat_1716, retro_fcat_1848, retro_fcat_267, retro_fcat_831,
Gorilla gorilla	ENSGGOG00000002870	8 retrocopies	retro_ggor_1215, retro_ggor_1680, retro_ggor_1868, retro_ggor_1933, retro_ggor_195, retro_ggor_227, retro_ggor_2775, retro_ggor_2940,
Macropus eugenii	ENSMEUG00000003228	2 retrocopies	retro_meug_36, retro_meug_49,
Macaca mulatta	ENSMMUG00000028844	6 retrocopies	retro_mmul_1416, retro_mmul_1591, retro_mmul_2233, retro_mmul_2547, retro_mmul_292, retro_mmul_364,
Monodelphis domestica	ENSMODG00000019167	2 retrocopies	retro_mdom_349, retro_mdom_680,
Mustela putorius furo	ENSMPUG00000015786	4 retrocopies	retro_mputfur_1007, retro_mputfur_1189, retro_mputfur_1574, retro_mputfur_457,
Pongo abelii	ENSPPYG00000009725	10 retrocopies	retro_pabe_1200, retro_pabe_1319, retro_pabe_1620, retro_pabe_2239, retro_pabe_2302, retro_pabe_3680, retro_pabe_3717, retro_pabe_3802, retro_pabe_482, retro_pabe_487,
Pan troglodytes	ENSPTRG00000010686	3 retrocopies	retro_ptro_1078, retro_ptro_1803, retro_ptro_27,
Pteropus vampyrus	ENSPVAG00000017378	6 retrocopies	retro_pvam_1314, retro_pvam_133, retro_pvam_155, retro_pvam_200, retro_pvam_607, retro_pvam_828,
Sarcophilus harrisii	ENSSHAG00000000406	3 retrocopies	retro_shar_435, retro_shar_474, retro_shar_706,
Sus scrofa	ENSSSCG00000013889	2 retrocopies	retro_sscr_1103, retro_sscr_184 ,
Tursiops truncatus	ENSTTRG00000008977	2 retrocopies	retro_ttru_151, retro_ttru_508,