RetrogeneDB ID: retro_sscr_677

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:91109834..91110260(-)
• Located in intron of: ENSSSCG00000014126

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000014569
• Aliases: None
• Description: None

Sequence

>retro_sscr_677
CCATCCAGACTAAGGAAGACCCAGAAACTTCAGGTCCACATGAGCCACGGCCGCATCAGCAAACACCAGAAGCACCCAGG
AGGCCGGGGGCAATGAGGGTGGCCTGCATCAGCACAGGATCAACTTTGACAAATGATTCTTTGGGAAAGCTGGAATGAGG
CAATACCACTTAAAGAGGAACCAGAGCATCTGCCCAAGTGTCAACCTTGATAAATGTGGACCTTGGTCAGCAAGCAGACA
CGGGTAAATGCTGCAAAAAACAAGACTGGAGATGCTCCTATCATTGACGTGGTGTGATTGTGTTACTACAAAGTTCTGGG
GAAGGAAAAGCTCCCAAAGCAGCCCGTCATCGTGAAAGCCAAATTTTTCAGCAGAGGAGCTGAAGAGAAGATTAAGGGTG
TGGGTGGGGCCTGTGTCCTGGTAGCT

Alignment

ORF - retro_sscr_677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.18 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRG-NAGGMHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFC
          PSRLRKT.KL..H.SHG..RI.KH.KHPGGRG.N.GG.H.HRIN........FGK.GMR.YHLKRNQS.C
Retrocopy PSRLRKTQKLQVHMSHG--RISKHQKHPGGRG>NEGGLHQHRIN---FDK*FFGKAGMRQYHLKRNQSIC

Parental  PTVNLDK-LWTLVSEQTRINAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKG
          P.VNLDK..WTLVS.QTR.NAAKNKTG.APIIDVV...YYKVLGK.KLPKQPVIVKAKFFSR.AEEKIKG
Retrocopy PSVNLDK<MWTLVSKQTRVNAAKNKTGDAPIIDVV*LCYYKVLGKEKLPKQPVIVKAKFFSRGAEEKIKG

Parental  VGGACVLVA
          VGGACVLVA
Retrocopy VGGACVLVA

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	230.29 RPM
SRP014902_testis	0.14 RPM	256.44 RPM
SRP018288_heart	0.00 RPM	208.27 RPM
SRP018288_kidney	0.00 RPM	214.84 RPM
SRP018288_liver	0.00 RPM	448.23 RPM
SRP018288_lung	0.00 RPM	205.38 RPM
SRP018856_adipose	0.00 RPM	219.29 RPM
SRP035408_brain	0.00 RPM	114.27 RPM
SRP035408_liver	0.00 RPM	176.75 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_677 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_677 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_677 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004205	15 retrocopies	retro_amel_1095, retro_amel_1160, retro_amel_1165, retro_amel_130, retro_amel_1311, retro_amel_1441, retro_amel_1673, retro_amel_393, retro_amel_450, retro_amel_497, retro_amel_521, retro_amel_693, retro_amel_752, retro_amel_966, retro_amel_989,
Bos taurus	ENSBTAG00000005349	2 retrocopies	retro_btau_126, retro_btau_45,
Canis familiaris	ENSCAFG00000006936	2 retrocopies	retro_cfam_145, retro_cfam_384,
Callithrix jacchus	ENSCJAG00000011775	1 retrocopy	retro_cjac_211,
Equus caballus	ENSECAG00000022469	1 retrocopy	retro_ecab_289,
Ficedula albicollis	ENSFALG00000000924	1 retrocopy	retro_falb_20,
Felis catus	ENSFCAG00000008411	13 retrocopies	retro_fcat_1162, retro_fcat_1285, retro_fcat_1305, retro_fcat_1380, retro_fcat_1635, retro_fcat_1761, retro_fcat_1805, retro_fcat_1974, retro_fcat_469, retro_fcat_652, retro_fcat_673, retro_fcat_817, retro_fcat_907,
Loxodonta africana	ENSLAFG00000000425	2 retrocopies	retro_lafr_25, retro_lafr_50,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Monodelphis domestica	ENSMODG00000007480	1 retrocopy	retro_mdom_575,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Oryctolagus cuniculus	ENSOCUG00000005442	1 retrocopy	retro_ocun_12,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Sus scrofa	ENSSSCG00000014569	9 retrocopies	retro_sscr_527, retro_sscr_574, retro_sscr_587, retro_sscr_588, retro_sscr_644, retro_sscr_668, retro_sscr_677 , retro_sscr_769, retro_sscr_809,
Tupaia belangeri	ENSTBEG00000000046	20 retrocopies	retro_tbel_1093, retro_tbel_1101, retro_tbel_1148, retro_tbel_1152, retro_tbel_1223, retro_tbel_1338, retro_tbel_1639, retro_tbel_2017, retro_tbel_2606, retro_tbel_2777, retro_tbel_298, retro_tbel_3111, retro_tbel_3496, retro_tbel_3881, retro_tbel_4566, retro_tbel_460, retro_tbel_544, retro_tbel_643, retro_tbel_925, retro_tbel_937,
Taeniopygia guttata	ENSTGUG00000008355	1 retrocopy	retro_tgut_18,