RetrogeneDB ID: retro_sscr_104

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:35412722..35413174(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000004197
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000014125
• Aliases: None
• Description: Sus scrofa dihydrofolate reductase (DHFR), mRNA. [Source:RefSeq mRNA;Acc:NM_001244064]

Sequence

>retro_sscr_104
ATGGTTCGTCCGCTAAACTGCATCGTTGCTGTGCCCCAGAACATGGGCTTCGGCAAGAACGAGGACCTGCCCTGGCCTCC
ACTCAGGAATGACTACAAATGTTTCCAAAGAATGACCACAACCTCTTCAGTAGAAGGCAAACAGAATTTGGTGACTATGG
GTAGGAAGACCTGGTTTCCATTCCAGAGAAGAATTGACCTTTAAAGGACAGAATTAATACAGTTCTCAGTAGAGAACTCA
AGGAACCTCCACAGGGAGCTCATTTTCTTGCCAAAAGTCTGGATGATGCCTTAAAACTTACTGAGAAGCCAGAATTAAAA
AATAAAGTGGACATGGTTTGGCTAGTGGGAGGCAGTTCAGTTTATAAGGAAGCCATGAACAAGCCAGGCCATCTTAGACT
TTTTGTGACAAGGATCATGAAAGAATTTGAAAGTGACACATTTTTTTCCCAG

Alignment

ORF - retro_sscr_104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.13 %
• Parental protein coverage: 80.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVRPLNCIVAVSQNMGIGKNGDLPWPPLRNEYK-YQRMTTTSSVEGKQNLVIMGRKTWF-SIPEKNRPLK
          MVRPLNCIVAV.QNMG.GKN.DLPWPPLRN.YK..QRMTTTSSVEGKQNLV.MGRKTWF.SIPEKN.PLK
Retrocopy MVRPLNCIVAVPQNMGFGKNEDLPWPPLRNDYKCFQRMTTTSSVEGKQNLVTMGRKTWF<SIPEKN*PLK

Parental  DRINIVLSRELKEPPQGAHFLAKSLDDALKLTEQPELKNKVDMVWIVGGSSVYKEAMNKPGHIRLFVTRI
          DRIN.VLSRELKEPPQGAHFLAKSLDDALKLTE.PELKNKVDMVW.VGGSSVYKEAMNKPGH.RLFVTRI
Retrocopy DRINTVLSRELKEPPQGAHFLAKSLDDALKLTEKPELKNKVDMVWLVGGSSVYKEAMNKPGHLRLFVTRI

Parental  MKEFESDTFFPE
          MKEFESDTFF..
Retrocopy MKEFESDTFFSQ

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	1.86 RPM
SRP014902_testis	0.00 RPM	7.50 RPM
SRP018288_heart	0.00 RPM	7.02 RPM
SRP018288_kidney	0.00 RPM	21.08 RPM
SRP018288_liver	0.00 RPM	31.82 RPM
SRP018288_lung	0.00 RPM	14.66 RPM
SRP018856_adipose	0.00 RPM	4.45 RPM
SRP035408_brain	0.00 RPM	6.29 RPM
SRP035408_liver	0.00 RPM	20.55 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_104 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015750	2 retrocopies	retro_amel_218, retro_amel_842,
Bos taurus	ENSBTAG00000007681	1 retrocopy	retro_btau_351,
Callithrix jacchus	ENSCJAG00000019556	4 retrocopies	retro_cjac_2017, retro_cjac_2298, retro_cjac_2446, retro_cjac_531,
Equus caballus	ENSECAG00000026827	1 retrocopy	retro_ecab_513,
Felis catus	ENSFCAG00000026745	3 retrocopies	retro_fcat_579, retro_fcat_705, retro_fcat_841,
Homo sapiens	ENSG00000228716	4 retrocopies	retro_hsap_1927, retro_hsap_2119, retro_hsap_3602, retro_hsap_6,
Gorilla gorilla	ENSGGOG00000022366	2 retrocopies	retro_ggor_1959, retro_ggor_2429,
Myotis lucifugus	ENSMLUG00000012200	2 retrocopies	retro_mluc_1109, retro_mluc_2577,
Macaca mulatta	ENSMMUG00000018283	13 retrocopies	retro_mmul_1496, retro_mmul_425, retro_mmul_692, retro_mmul_693, retro_mmul_695, retro_mmul_700, retro_mmul_701, retro_mmul_704, retro_mmul_738, retro_mmul_760, retro_mmul_768, retro_mmul_82, retro_mmul_994,
Monodelphis domestica	ENSMODG00000024860	3 retrocopies	retro_mdom_1685, retro_mdom_604, retro_mdom_703,
Mustela putorius furo	ENSMPUG00000008704	1 retrocopy	retro_mputfur_1107,
Mus musculus	ENSMUSG00000021707	1 retrocopy	retro_mmus_3326,
Nomascus leucogenys	ENSNLEG00000012989	3 retrocopies	retro_nleu_1193, retro_nleu_2314, retro_nleu_2631,
Oryctolagus cuniculus	ENSOCUG00000005127	3 retrocopies	retro_ocun_1351, retro_ocun_1640, retro_ocun_650,
Otolemur garnettii	ENSOGAG00000025320	1 retrocopy	retro_ogar_222,
Pongo abelii	ENSPPYG00000015600	2 retrocopies	retro_pabe_2959, retro_pabe_41,
Pan troglodytes	ENSPTRG00000017042	3 retrocopies	retro_ptro_109, retro_ptro_1551, retro_ptro_2988,
Rattus norvegicus	ENSRNOG00000013521	1 retrocopy	retro_rnor_2030,
Sus scrofa	ENSSSCG00000014125	2 retrocopies	retro_sscr_104 , retro_sscr_1131,