RetrogeneDB ID: retro_sscr_372

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:70328504..70329143(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRELID1
• Ensembl ID: ENSSSCG00000014042
• Aliases: None
• Description: PRELI domain containing 1 [Source:HGNC Symbol;Acc:30255]

Sequence

>retro_sscr_372
GTGGTGAAGTATTTCCTGGGCCAGAGAGTGCTCCAGAGTTCCTGGGCCCAAGTGTTGGCTGCCTTCTGGCAGCATACCTG
AATCCCTATAGCAAACATGTCTTGACAGAAGACATAGTGCACAGGGAGGTGACCCCTGATCAGAAGCTCCTGTCCCAGTG
ACTCCTGATGAAGACCATCAGAATGCCCTTCTGGGCTGAGTGACTGTTTCCTGCCAGTGTTGCTCACTCAGTGCACATCC
TGGAGAATTCTATTGTGGACCCTCAGAACCAGACCATGATCACTTTCACCTGGAACATCAACTACACCCAGCGGATGGTG
GTGGAGGAACGATGTGTTTATGGTGTGAACTCTGATAACAATGGCTAGACTGCAATCCAACAGGAAGCCTGGGTCTCCTC
TAGCTTATTTGGCATCTCCAGAGCTGTCCAGGAACTTGGTCTCACGTGGTTCAAAAGTGACCAAGACTATGAAGAATTTT
GAATATATCTTGGCCAAGCTGAAAGTGAGACCCCTCCCTAAATCCTTGTTTGAAACAGCCAAGGAAGCCAAGGAGAAGGC
CAAGGAGATGGCACTGGCAGCTACAGAGAAGGCCAAGGACCTTGCCAGCAAGGCAGCCACCAAGAAGCAGCAGCAGCAG

Alignment

ORF - retro_sscr_372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.58 %
• Parental protein coverage: 98.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVKYFLGQSVLRSSWDQVFAAFWQR-YPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERL
          .VKYFLGQ.VL.SSW.QV.AAFWQ..Y.NPYSKHVLTEDIVHREVTPDQKLLS..LL.KT.RMP.WAE.L
Retrocopy VVKYFLGQRVLQSSWAQVLAAFWQH<YLNPYSKHVLTEDIVHREVTPDQKLLSQ*LLMKTIRMPFWAE*L

Parental  FPANVAHSVYILEDSIVDPQNQTMTTFTWNINHARLMVVEERCVYRVNSDNNSWTEIRREAWVSSSLFGV
          FPA.VAHSV.ILE.SIVDPQNQTM.TFTWNIN....MVVEERCVY.VNSDNN..T.I..EAWVSSSLFG.
Retrocopy FPASVAHSVHILENSIVDPQNQTMITFTWNINYTQRMVVEERCVYGVNSDNNG*TAIQQEAWVSSSLFGI

Parental  SRAVQEFGLARFKSNVTKTMKGFEYILAKLQGEAP-PKTLVETAKEAKEKAKETALAATEKAKDLASKAA
          SRAVQE.GL..FKS........F...L.....E.P.PK.L.ETAKEAKEKAKE.ALAATEKAKDLASKAA
Retrocopy SRAVQELGLTWFKSD--QDYEEF*IYLGQAESETP>PKSLFETAKEAKEKAKEMALAATEKAKDLASKAA

Parental  TKKQQQQ
          TKKQQQQ
Retrocopy TKKQQQQ

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	226.97 RPM
SRP014902_testis	0.00 RPM	110.33 RPM
SRP018288_heart	0.03 RPM	21.98 RPM
SRP018288_kidney	0.00 RPM	155.64 RPM
SRP018288_liver	0.00 RPM	163.59 RPM
SRP018288_lung	0.00 RPM	86.45 RPM
SRP018856_adipose	0.00 RPM	125.38 RPM
SRP035408_brain	0.00 RPM	74.16 RPM
SRP035408_liver	0.00 RPM	180.30 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_372 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_372 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005009	2 retrocopies	retro_btau_1727, retro_btau_962,
Canis familiaris	ENSCAFG00000016443	2 retrocopies	retro_cfam_2055, retro_cfam_349,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Homo sapiens	ENSG00000169230	7 retrocopies	retro_hsap_1550, retro_hsap_2269, retro_hsap_249, retro_hsap_302, retro_hsap_3518, retro_hsap_3565, retro_hsap_579,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mustela putorius furo	ENSMPUG00000012226	1 retrocopy	retro_mputfur_579,
Nomascus leucogenys	ENSNLEG00000012714	5 retrocopies	retro_nleu_1382, retro_nleu_2395, retro_nleu_2400, retro_nleu_803, retro_nleu_857,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Pongo abelii	ENSPPYG00000016086	7 retrocopies	retro_pabe_1283, retro_pabe_1696, retro_pabe_1699, retro_pabe_2907, retro_pabe_377, retro_pabe_409, retro_pabe_608,
Sus scrofa	ENSSSCG00000014042	4 retrocopies	retro_sscr_372 , retro_sscr_794, retro_sscr_795, retro_sscr_811,
Tupaia belangeri	ENSTBEG00000006445	1 retrocopy	retro_tbel_3855,
Tursiops truncatus	ENSTTRG00000009571	1 retrocopy	retro_ttru_1886,