RetrogeneDB ID: retro_sscr_603

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 18:53180549..53180884(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPP19
• Ensembl ID: ENSSSCG00000004618
• Aliases: ARPP-19, Arpp19
• Description: Sus scrofa cAMP-regulated phosphoprotein (ARPP-19), mRNA. [Source:RefSeq mRNA;Acc:NM_214175]

Sequence

>retro_sscr_603
ATGTCTGTGGGAGCCCCCGAGGCAGCCTCCACGGAGGAGCAGAAGGAAATGGAAGATAAAGTGATGAGTCCAGAGAAAAC
TGAAGAAGCAACGTTAAAGCAAGGTGTTCCCATCTGGGACAAAAGCCTGGAGGTTCAGGTTTCCTAAGGAAATAGTTGCA
GAAAGGGCAGCAATATTCTGAGTCTGGGGATTATAGCGTGGCTAAAGCAAAAACGAAGAACAAGCAATCTCCCAGTGCCA
CCCAAGATAAGACAGAGGCCACCCGTGACCACATTCCCACTTGGCAGGAGCTTCCTCAACAGAAACCCTCTCTTGCTGCT
AGCAAGCTGGCTGGC

Alignment

ORF - retro_sscr_603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAEVPEAASAEEQKEMEDKVTSPEKAEEAKLK-ARYPHLGQKPGGSDFLRKRLQKGQKYFDSGDYNMAK
          MS...PEAAS.EEQKEMEDKV.SPEK.EEA.LK.AR..HLGQKPGGS.FLRK.LQKGQ.Y..SGDY..AK
Retrocopy MSVGAPEAASTEEQKEMEDKVMSPEKTEEATLK<ARCSHLGQKPGGSGFLRK*LQKGQQYSESGDYSVAK

Parental  AKMKNKQLPTAAPDKTEVTGDHIPTPQDLPQRKPSLVASKLAG
          AK.KNKQ.P.A..DKTE.T.DHIPT.Q.LPQ.KPSL.ASKLAG
Retrocopy AKTKNKQSPSATQDKTEATRDHIPTWQELPQQKPSLAASKLAG

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	13.54 RPM
SRP014902_testis	0.00 RPM	26.45 RPM
SRP018288_heart	0.00 RPM	74.05 RPM
SRP018288_kidney	0.00 RPM	60.58 RPM
SRP018288_liver	0.00 RPM	18.87 RPM
SRP018288_lung	0.10 RPM	69.95 RPM
SRP018856_adipose	0.00 RPM	34.73 RPM
SRP035408_brain	0.00 RPM	86.01 RPM
SRP035408_liver	0.00 RPM	14.91 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_603 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_603 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_603 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011022	5 retrocopies	retro_btau_1259, retro_btau_1821, retro_btau_1845, retro_btau_952, retro_btau_981,
Canis familiaris	ENSCAFG00000032515	2 retrocopies	retro_cfam_1375, retro_cfam_1402,
Cavia porcellus	ENSCPOG00000011228	1 retrocopy	retro_cpor_1148,
Dasypus novemcinctus	ENSDNOG00000004474	9 retrocopies	retro_dnov_1086, retro_dnov_1576, retro_dnov_1960, retro_dnov_2150, retro_dnov_2427, retro_dnov_557, retro_dnov_616, retro_dnov_644, retro_dnov_662,
Dipodomys ordii	ENSDORG00000011321	2 retrocopies	retro_dord_194, retro_dord_33,
Echinops telfairi	ENSETEG00000015550	1 retrocopy	retro_etel_585,
Homo sapiens	ENSG00000128989	2 retrocopies	retro_hsap_2130, retro_hsap_3280,
Gorilla gorilla	ENSGGOG00000025250	1 retrocopy	retro_ggor_198,
Nomascus leucogenys	ENSNLEG00000006551	2 retrocopies	retro_nleu_2533, retro_nleu_2884,
Oryctolagus cuniculus	ENSOCUG00000015489	10 retrocopies	retro_ocun_1182, retro_ocun_1297, retro_ocun_1398, retro_ocun_1573, retro_ocun_1731, retro_ocun_1768, retro_ocun_310, retro_ocun_473, retro_ocun_479, retro_ocun_698,
Otolemur garnettii	ENSOGAG00000013865	1 retrocopy	retro_ogar_591,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923,
Pan troglodytes	ENSPTRG00000042183	1 retrocopy	retro_ptro_1559,
Sus scrofa	ENSSSCG00000004618	1 retrocopy	retro_sscr_603 ,
Ictidomys tridecemlineatus	ENSSTOG00000003677	7 retrocopies	retro_itri_1075, retro_itri_1290, retro_itri_1339, retro_itri_1643, retro_itri_1657, retro_itri_1865, retro_itri_594,
Tursiops truncatus	ENSTTRG00000004804	1 retrocopy	retro_ttru_172,