RetrogeneDB ID: retro_sscr_228

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:58921098..58921543(+)
• Located in intron of: ENSSSCG00000011085

Retrocopy information

• Ensembl ID: ENSSSCG00000029019
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CALM1
• Ensembl ID: ENSSSCG00000008433
• Aliases: None
• Description: None

Sequence

>retro_sscr_228
ATGGCTGATCAACTGACCGAAGAACAGACTGCTGAATTCAAGGAAGCTTTCTCCCTATTTGACAAAGATGGAGATGGCAC
CATCACAACAAAGGAACTTGGAACTGTCACAAGGTCATTGGGTCAGAACCCGACAGAAGCTGAGTTGCAGGATATGATCA
ATGAGGTGGACGCTGATGGTAATGGTACCACTGACTTCCCTGAATTTTTTACTATGATGGCTAGAAAAATTAAAGACAGA
CAGCAAAGAAGAAATCCACGAGGCATTCTGAGTCTTTGACAAGGATGGCAATGGCTACATCAGTGCTGCAGAACTATGTC
ACGTCATGACAAACTTAGGAGAAAAACTAACAGACGAAGAAGTAGATGAAATGATCAGAGAAGCAGATATGGATGGAGAT
GGACGAGTCAACTACGAAGAATTTGTACAGATGATGACTGCAAAA

Alignment

ORF - retro_sscr_228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
          MADQLTEEQ.AEFKEAFSLFDKDGDGTITTKELGTV.RSLGQNPTEAELQDMINEVDADGNGT.DFPEF.
Retrocopy MADQLTEEQTAEFKEAFSLFDKDGDGTITTKELGTVTRSLGQNPTEAELQDMINEVDADGNGTTDFPEFF

Parental  TMMARKMKD-TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNY
          TMMARK.KD....EE.I.EAF.VFDKDGNGYISAAEL.HVMTNLGEKLTDEEVDEMIREAD.DGDG.VNY
Retrocopy TMMARKIKD>DSKEE-IHEAF*VFDKDGNGYISAAELCHVMTNLGEKLTDEEVDEMIREADMDGDGRVNY

Parental  EEFVQMMTAK
          EEFVQMMTAK
Retrocopy EEFVQMMTAK

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	0.13 RPM	198.30 RPM
SRP014902_testis	0.00 RPM	147.95 RPM
SRP018288_heart	0.00 RPM	306.20 RPM
SRP018288_kidney	0.20 RPM	345.16 RPM
SRP018288_liver	0.00 RPM	218.28 RPM
SRP018288_lung	0.00 RPM	187.16 RPM
SRP018856_adipose	0.37 RPM	231.08 RPM
SRP035408_brain	0.51 RPM	1957.08 RPM
SRP035408_liver	0.03 RPM	346.49 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_228 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_228 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 35 parental genes, and 132 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015712	1 retrocopy	retro_acar_45,
Ailuropoda melanoleuca	ENSAMEG00000006204	2 retrocopies	retro_amel_63, retro_amel_72,
Choloepus hoffmanni	ENSCHOG00000008245	6 retrocopies	retro_chof_1940, retro_chof_2261, retro_chof_367, retro_chof_735, retro_chof_833, retro_chof_965,
Callithrix jacchus	ENSCJAG00000000638	4 retrocopies	retro_cjac_1039, retro_cjac_1401, retro_cjac_2859, retro_cjac_4097,
Cavia porcellus	ENSCPOG00000012181	3 retrocopies	retro_cpor_1012, retro_cpor_87, retro_cpor_89,
Equus caballus	ENSECAG00000008396	4 retrocopies	retro_ecab_15, retro_ecab_59, retro_ecab_750, retro_ecab_882,
Erinaceus europaeus	ENSEEUG00000000040	3 retrocopies	retro_eeur_38, retro_eeur_561, retro_eeur_671,
Echinops telfairi	ENSETEG00000009377	5 retrocopies	retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Echinops telfairi	ENSETEG00000018667	16 retrocopies	retro_etel_1032, retro_etel_1075, retro_etel_108, retro_etel_1164, retro_etel_1184, retro_etel_1507, retro_etel_1650, retro_etel_1683, retro_etel_1903, retro_etel_2139, retro_etel_22, retro_etel_539, retro_etel_687, retro_etel_864, retro_etel_902, retro_etel_951,
Ficedula albicollis	ENSFALG00000012828	1 retrocopy	retro_falb_16,
Felis catus	ENSFCAG00000029141	5 retrocopies	retro_fcat_1926, retro_fcat_591, retro_fcat_629, retro_fcat_87, retro_fcat_88,
Gadus morhua	ENSGMOG00000009342	1 retrocopy	retro_gmor_23,
Latimeria chalumnae	ENSLACG00000005059	1 retrocopy	retro_lcha_53,
Loxodonta africana	ENSLAFG00000009865	1 retrocopy	retro_lafr_655,
Myotis lucifugus	ENSMLUG00000029016	6 retrocopies	retro_mluc_13, retro_mluc_1732, retro_mluc_18, retro_mluc_19, retro_mluc_2207, retro_mluc_2258,
Macaca mulatta	ENSMMUG00000017466	1 retrocopy	retro_mmul_256,
Monodelphis domestica	ENSMODG00000009222	1 retrocopy	retro_mdom_1126,
Mustela putorius furo	ENSMPUG00000012061	4 retrocopies	retro_mputfur_1207, retro_mputfur_21, retro_mputfur_838, retro_mputfur_942,
Nomascus leucogenys	ENSNLEG00000016954	3 retrocopies	retro_nleu_118, retro_nleu_2563, retro_nleu_2862,
Oryctolagus cuniculus	ENSOCUG00000002107	2 retrocopies	retro_ocun_1468, retro_ocun_84,
Otolemur garnettii	ENSOGAG00000008824	6 retrocopies	retro_ogar_1126, retro_ogar_1196, retro_ogar_1432, retro_ogar_1535, retro_ogar_209, retro_ogar_2326,
Ochotona princeps	ENSOPRG00000015478	7 retrocopies	retro_opri_1129, retro_opri_1155, retro_opri_16, retro_opri_40, retro_opri_506, retro_opri_830, retro_opri_86,
Petromyzon marinus	ENSPMAG00000003323	1 retrocopy	retro_pmar_12,
Pongo abelii	ENSPPYG00000012430	5 retrocopies	retro_pabe_1068, retro_pabe_1133, retro_pabe_115, retro_pabe_45, retro_pabe_599,
Pelodiscus sinensis	ENSPSIG00000013173	1 retrocopy	retro_psin_9,
Pan troglodytes	ENSPTRG00000011901	4 retrocopies	retro_ptro_1195, retro_ptro_2623, retro_ptro_83, retro_ptro_881,
Pteropus vampyrus	ENSPVAG00000005183	2 retrocopies	retro_pvam_558, retro_pvam_560,
Sorex araneus	ENSSARG00000008731	1 retrocopy	retro_sara_119,
Sus scrofa	ENSSSCG00000008433	1 retrocopy	retro_sscr_228 ,
Sus scrofa	ENSSSCG00000025768	3 retrocopies	retro_sscr_26, retro_sscr_390, retro_sscr_692,
Ictidomys tridecemlineatus	ENSSTOG00000021814	7 retrocopies	retro_itri_1048, retro_itri_1473, retro_itri_37, retro_itri_433, retro_itri_68, retro_itri_778, retro_itri_859,
Tupaia belangeri	ENSTBEG00000000569	17 retrocopies	retro_tbel_1450, retro_tbel_24, retro_tbel_2418, retro_tbel_258, retro_tbel_2612, retro_tbel_2856, retro_tbel_2933, retro_tbel_3150, retro_tbel_3195, retro_tbel_3956, retro_tbel_4141, retro_tbel_4171, retro_tbel_4212, retro_tbel_4324, retro_tbel_675, retro_tbel_722, retro_tbel_765,
Taeniopygia guttata	ENSTGUG00000002581	1 retrocopy	retro_tgut_6,
Tarsius syrichta	ENSTSYG00000012564	5 retrocopies	retro_tsyr_1641, retro_tsyr_2012, retro_tsyr_2128, retro_tsyr_2148, retro_tsyr_576,
Vicugna pacos	ENSVPAG00000009286	1 retrocopy	retro_vpac_442,