RetrogeneDB ID: retro_sscr_161

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:83659974..83660433(-)
• Located in intron of: ENSSSCG00000024176

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLMO2
• Ensembl ID: ENSSSCG00000007525
• Aliases: SLMO2, C17H20orf45
• Description: Sus scrofa slowmo homolog 2 (Drosophila) (SLMO2), mRNA. [Source:RefSeq mRNA;Acc:NM_001113697]

Sequence

>retro_sscr_161
GACCACCCATGGGAAACTGTTACAACAGCTGCAATGCAGAAATACTCAAACCTTGTGAACTCAGTGTGGCTGGAGTTAAT
GTATTGCACAGACATAGAGATCCCTCTAGAAAGCTACACAACCAAAGATTCCTCAGCACAGAGTGGGGACTGCCTTCCAT
TGTGATATCTCTTATTGGTGCAGCAGGAACTAAAACATATGTGAAGAACATATGTGAGTGGATCCTGTAGAGAAAACAAC
AGAACTTAAATCTAATATTTCATTTACAAATACAGCTCCAGGAGATGAGAGACATATACAAACCACATTCTTAAGACCCA
GAAAAAAACTGTTTTTACTCAAGAATTCTTAATTGCCATTGAAAGGAGTCAGTCTCAGCACTCTGAAGGGCTGATGGCAA
GTATATCTTCAAGTGTTAATAAATTTAGCTGAGAAGCAACAGAATAGGTAATACATAAA

Alignment

ORF - retro_sscr_161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 80.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DHPWETVTTAAMQKYPNPMNP-SVVGVDVLDRHIDASGKLHSHRLLSTEWGLPSIVKSIIGAARTKTYV-
          DHPWETVTTAAMQKY.N..N..SV.GV.VL.RH.D.S.KLH..R.LSTEWGLPSIV.S.IGAA.TKTYV.
Retrocopy DHPWETVTTAAMQKYSNLVNS<SVAGVNVLHRHRDPSRKLHNQRFLSTEWGLPSIVISLIGAAGTKTYV<

Parental  QEHSVVDPVAKTMELKSTNISFTNMVSVDERLIYKPHPQDSEKTVLTQEAIITVKGVSLGSYLEG-LMAS
          .EH..VDPV.KT.ELKS.NISFTN....DER.I.........K..L........KGVSL.S.L.G.LMAS
Retrocopy EEHM*VDPVEKTTELKS-NISFTNTAPGDERHIQTTFLRPRKKLFLLKNS*LPLKGVSL-STLKG<LMAS

Parental  TISSNANK-GREAMEWVIHK
          .ISS..NK...EA.E.VIHK
Retrocopy -ISSSVNKFS*EATE*VIHK

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	12.48 RPM
SRP014902_testis	0.14 RPM	9.05 RPM
SRP018288_heart	0.00 RPM	13.07 RPM
SRP018288_kidney	0.00 RPM	24.04 RPM
SRP018288_liver	0.00 RPM	9.75 RPM
SRP018288_lung	0.00 RPM	17.11 RPM
SRP018856_adipose	0.09 RPM	6.39 RPM
SRP035408_brain	0.00 RPM	2.73 RPM
SRP035408_liver	0.00 RPM	5.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_161 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_161 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_161 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004402	3 retrocopies	retro_btau_1006, retro_btau_1346, retro_btau_996,
Canis familiaris	ENSCAFG00000012220	1 retrocopy	retro_cfam_1293,
Callithrix jacchus	ENSCJAG00000018905	4 retrocopies	retro_cjac_1286, retro_cjac_2921, retro_cjac_3171, retro_cjac_3236,
Cavia porcellus	ENSCPOG00000012397	4 retrocopies	retro_cpor_1285, retro_cpor_1412, retro_cpor_456, retro_cpor_468,
Dasypus novemcinctus	ENSDNOG00000014548	3 retrocopies	retro_dnov_1402, retro_dnov_2032, retro_dnov_2311,
Equus caballus	ENSECAG00000000513	1 retrocopy	retro_ecab_409,
Erinaceus europaeus	ENSEEUG00000003697	4 retrocopies	retro_eeur_244, retro_eeur_34, retro_eeur_389, retro_eeur_406,
Felis catus	ENSFCAG00000031431	1 retrocopy	retro_fcat_1499,
Homo sapiens	ENSG00000101166	6 retrocopies	retro_hsap_310, retro_hsap_3166, retro_hsap_3167, retro_hsap_3311, retro_hsap_3783, retro_hsap_4227,
Gorilla gorilla	ENSGGOG00000004803	5 retrocopies	retro_ggor_1349, retro_ggor_1350, retro_ggor_2544, retro_ggor_2545, retro_ggor_2830,
Microcebus murinus	ENSMICG00000014902	12 retrocopies	retro_mmur_101, retro_mmur_1111, retro_mmur_1143, retro_mmur_1299, retro_mmur_1304, retro_mmur_1318, retro_mmur_1391, retro_mmur_1400, retro_mmur_1604, retro_mmur_512, retro_mmur_659, retro_mmur_912,
Myotis lucifugus	ENSMLUG00000014907	2 retrocopies	retro_mluc_1887, retro_mluc_845,
Macaca mulatta	ENSMMUG00000007560	4 retrocopies	retro_mmul_1155, retro_mmul_1644, retro_mmul_2123, retro_mmul_539,
Monodelphis domestica	ENSMODG00000016608	5 retrocopies	retro_mdom_1596, retro_mdom_1619, retro_mdom_1620, retro_mdom_1655, retro_mdom_405,
Mustela putorius furo	ENSMPUG00000007075	1 retrocopy	retro_mputfur_1586,
Nomascus leucogenys	ENSNLEG00000009579	3 retrocopies	retro_nleu_1118, retro_nleu_2497, retro_nleu_2498,
Oryctolagus cuniculus	ENSOCUG00000005621	8 retrocopies	retro_ocun_1944, retro_ocun_1954, retro_ocun_455, retro_ocun_486, retro_ocun_549, retro_ocun_619, retro_ocun_775, retro_ocun_926,
Otolemur garnettii	ENSOGAG00000013382	10 retrocopies	retro_ogar_1037, retro_ogar_1650, retro_ogar_2233, retro_ogar_2972, retro_ogar_3009, retro_ogar_3120, retro_ogar_3281, retro_ogar_3378, retro_ogar_3389, retro_ogar_3392,
Pongo abelii	ENSPPYG00000011182	7 retrocopies	retro_pabe_1462, retro_pabe_2631, retro_pabe_2632, retro_pabe_2731, retro_pabe_3089, retro_pabe_3411, retro_pabe_371,
Pan troglodytes	ENSPTRG00000013682	5 retrocopies	retro_ptro_2160, retro_ptro_2273, retro_ptro_251, retro_ptro_252, retro_ptro_2564,
Pteropus vampyrus	ENSPVAG00000005226	2 retrocopies	retro_pvam_1075, retro_pvam_1445,
Sus scrofa	ENSSSCG00000007525	3 retrocopies	retro_sscr_161 , retro_sscr_258, retro_sscr_959,
Tupaia belangeri	ENSTBEG00000000493	1 retrocopy	retro_tbel_1407,
Tarsius syrichta	ENSTSYG00000012533	2 retrocopies	retro_tsyr_2061, retro_tsyr_250,
Tursiops truncatus	ENSTTRG00000008417	2 retrocopies	retro_ttru_621, retro_ttru_818,
Vicugna pacos	ENSVPAG00000001044	2 retrocopies	retro_vpac_224, retro_vpac_359,