RetrogeneDB ID: retro_sscr_2

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:28015648..28016107(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000008767
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSSSCG00000001502
• Aliases: None
• Description: Sus scrofa ribosomal protein S18 (RPS18), mRNA. [Source:RefSeq mRNA;Acc:NM_213940]

Sequence

>retro_sscr_2
CTGTCTCTAGTAATCCTTGAGAAGTTCCAGCACATTTTGCGAGTACTCAACACCACCATTGATGGGTGGCAGAAAATTGC
CTTTGCTACCACTGCGATTAAGGGTGTAGGACGGAGATATGCTCACGTGGTGTTGAGGAAAGCAGACATTGACCTCACCA
AGAGGGCAGGAGAGCTCACAGAGGATGAGGTGGAACATGTAATCACCATTATGCAGAATCCAGGCCAATACAAGATTCCA
GACTGGTTCTTAAATAGACAGAAGGATGTGAAGGATGGGAAGTACAGCCAGGTCCTGGCCAACGGTCTGGATAACAAACT
CCATGAAGACGTGGAGCGACTGAAGAAGATTCGGGCCCACAGAGGGCTGCGCCACTTCTGGGGACTGCGTGTCGGAGGCC
AGCACACCAAGACCACAGGCCGCCGTGGCCACACCGTGCGTGTGTCCAAGAAGACATAA

Alignment

ORF - retro_sscr_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.39 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
          .SLVI.EKFQHILRVLNT.IDG..KIAFA.TAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVE.VITI
Retrocopy LSLVILEKFQHILRVLNTTIDGWQKIAFATTAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVEHVITI

Parental  MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
          MQNP.QYKIPDWFLNRQKDVKDGKYSQVLANGLDNKL.ED.ERLKKIRAHRGLRHFWGLRV.GQHTKTTG
Retrocopy MQNPGQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLHEDVERLKKIRAHRGLRHFWGLRVGGQHTKTTG

Parental  RRGRTVGVSKK
          RRG.TV.VSKK
Retrocopy RRGHTVRVSKK

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	615.61 RPM
SRP014902_testis	2.69 RPM	1480.24 RPM
SRP018288_heart	0.16 RPM	293.03 RPM
SRP018288_kidney	0.49 RPM	354.32 RPM
SRP018288_liver	0.96 RPM	346.68 RPM
SRP018288_lung	0.00 RPM	340.61 RPM
SRP018856_adipose	2.46 RPM	1001.25 RPM
SRP035408_brain	0.89 RPM	436.67 RPM
SRP035408_liver	1.00 RPM	396.57 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_2 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_2 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_2 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 138 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002648	2 retrocopies	retro_btau_1052, retro_btau_614,
Callithrix jacchus	ENSCJAG00000021650	5 retrocopies	retro_cjac_22, retro_cjac_245, retro_cjac_2529, retro_cjac_2893, retro_cjac_2955,
Dasypus novemcinctus	ENSDNOG00000012084	13 retrocopies	retro_dnov_1295, retro_dnov_1398, retro_dnov_1448, retro_dnov_1675, retro_dnov_1770, retro_dnov_2008, retro_dnov_2115, retro_dnov_2223, retro_dnov_2288, retro_dnov_327, retro_dnov_363, retro_dnov_384, retro_dnov_399,
Erinaceus europaeus	ENSEEUG00000010297	8 retrocopies	retro_eeur_201, retro_eeur_261, retro_eeur_380, retro_eeur_460, retro_eeur_473, retro_eeur_498, retro_eeur_667, retro_eeur_689,
Homo sapiens	ENSG00000231500	2 retrocopies	retro_hsap_1806, retro_hsap_1974,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Macropus eugenii	ENSMEUG00000016770	11 retrocopies	retro_meug_1296, retro_meug_1737, retro_meug_1807, retro_meug_1946, retro_meug_212, retro_meug_310, retro_meug_344, retro_meug_387, retro_meug_566, retro_meug_625, retro_meug_627,
Myotis lucifugus	ENSMLUG00000007360	2 retrocopies	retro_mluc_181, retro_mluc_932,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Monodelphis domestica	ENSMODG00000014210	4 retrocopies	retro_mdom_1041, retro_mdom_1286, retro_mdom_1514, retro_mdom_642,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Otolemur garnettii	ENSOGAG00000006225	7 retrocopies	retro_ogar_1498, retro_ogar_1832, retro_ogar_2372, retro_ogar_472, retro_ogar_608, retro_ogar_709, retro_ogar_905,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Pteropus vampyrus	ENSPVAG00000001902	6 retrocopies	retro_pvam_295, retro_pvam_556, retro_pvam_691, retro_pvam_708, retro_pvam_829, retro_pvam_875,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,
Sus scrofa	ENSSSCG00000001502	5 retrocopies	retro_sscr_112, retro_sscr_156, retro_sscr_157, retro_sscr_2 , retro_sscr_831,
Tupaia belangeri	ENSTBEG00000012708	40 retrocopies	retro_tbel_1070, retro_tbel_1739, retro_tbel_1745, retro_tbel_1806, retro_tbel_1818, retro_tbel_1827, retro_tbel_1855, retro_tbel_205, retro_tbel_2087, retro_tbel_211, retro_tbel_2299, retro_tbel_2309, retro_tbel_2312, retro_tbel_234, retro_tbel_2364, retro_tbel_2424, retro_tbel_2473, retro_tbel_250, retro_tbel_2682, retro_tbel_2768, retro_tbel_295, retro_tbel_3189, retro_tbel_3317, retro_tbel_3383, retro_tbel_3625, retro_tbel_363, retro_tbel_3686, retro_tbel_3731, retro_tbel_3870, retro_tbel_4100, retro_tbel_4215, retro_tbel_4365, retro_tbel_45, retro_tbel_4562, retro_tbel_4578, retro_tbel_462, retro_tbel_57, retro_tbel_578, retro_tbel_856, retro_tbel_941,
Tursiops truncatus	ENSTTRG00000004302	3 retrocopies	retro_ttru_1012, retro_ttru_1553, retro_ttru_837,