RetrogeneDB ID: retro_sscr_519

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:20194807..20195519(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000029253
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDRG3
• Ensembl ID: ENSSSCG00000007322
• Aliases: None
• Description: NDRG family member 3 [Source:HGNC Symbol;Acc:14462]

Sequence

>retro_sscr_519
AAGGAACATGATATAGAAACAACTCATGGATGGTCCATGTCACTATAAGAGGCTTACCAAAGGGAAACAGACCATTTATT
GGATATACCATACATTGGCCTCAATCATAAATCCTGTTTCAATGCATTCTTTAACTTTGAGGATATGCAAGAAATCACCC
AGCACTTTGCTGTCTGTCATGTGGATGCCCCAGACCAGAAGGAAGGTGCACCCTCTTTCCCAACTGGGTACCAGTACCCC
ACAATGGATGAGCGGGCCCAAATGCTACCTTCTGTTCTCACCCACTTAAATTCCAAAAGCATCACTGGGGTTGGAGTTGG
AGCTTACATCCTCAGCAGATTTGCTCTCAATCACCCAAAGCTTGTGGAAGGTCTCGTGCTCGTTAATGTTGACCCTTGTG
CTAAAGGCTGGATTGACTGGGCAGCTTCCAAACTCTCAGGATTGACAACCAATGTTGTGGACATTATTTTGGCTCATCAC
TTTGGGCAAGAAGAATTGCAAGCCAACCTGAACCTGATTCAAACCTACAGACTGCATATTGCCCAAGATATCAACCAAGA
AAACCTATAGCTCTTTCTGAGTTCTTATAACAGATACAAAGACTTGGAGATTGAAGACCCTCCTGGGACAAAATGGTAAC
AAATCAAAAACATTAAACTGTTCTACTTTATTGGTGGTAGGTGACAATTCACCTGGAGTTGAGGCTGTGGTT

Alignment

ORF - retro_sscr_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 88.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QEHDIETTHG-VVHVTIRGLPKGNRPVI-MTYHD-IGLNHKSCFNAFFNFEDMQEITQHFAVCHVDAPGQ
          .EHDIETTHG..VHVTIRGLPKGNRP.I...YH..IGLNHKSCFNAFFNFEDMQEITQHFAVCHVDAP.Q
Retrocopy KEHDIETTHG<MVHVTIRGLPKGNRPFI<WIYHT<IGLNHKSCFNAFFNFEDMQEITQHFAVCHVDAPDQ

Parental  QEGAPSFPSGYQYPTMDELAEMLPSVLTHLNLKSIIGVGVGAGAYILSRFALNHPELVEGLVLINVDPCA
          .EGAPSFP.GYQYPTMDE.A.MLPSVLTHLN.KSI.GVGVGA..YILSRFALNHP.LVEGLVL.NVDPCA
Retrocopy KEGAPSFPTGYQYPTMDERAQMLPSVLTHLNSKSITGVGVGA--YILSRFALNHPKLVEGLVLVNVDPCA

Parental  KGWIDWAASKLSGLTTNVVDIILAHHFGQEELQANLDLIQTYRLHIAQDINQENLQLFLSSYNGRKDLEI
          KGWIDWAASKLSGLTTNVVDIILAHHFGQEELQANL.LIQTYRLHIAQDINQENL.LFLSSYN..KDLEI
Retrocopy KGWIDWAASKLSGLTTNVVDIILAHHFGQEELQANLNLIQTYRLHIAQDINQENL*LFLSSYNRYKDLEI

Parental  E-RP-ILGQNDNKSKTLKCSTLLVVGDNSPAVEAVV
          E.RP..LGQN.NKSKTL.CSTLLVVGDNSP.VEAVV
Retrocopy E<RP<LLGQNGNKSKTLNCSTLLVVGDNSPGVEAVV

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	4.38 RPM
SRP014902_testis	0.00 RPM	10.61 RPM
SRP018288_heart	0.03 RPM	5.24 RPM
SRP018288_kidney	0.10 RPM	17.93 RPM
SRP018288_liver	0.00 RPM	2.40 RPM
SRP018288_lung	0.10 RPM	10.49 RPM
SRP018856_adipose	0.00 RPM	7.74 RPM
SRP035408_brain	0.00 RPM	33.92 RPM
SRP035408_liver	0.00 RPM	2.03 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_519 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_519 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_519 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012562	1 retrocopy	retro_amel_378,
Echinops telfairi	ENSETEG00000002250	1 retrocopy	retro_etel_2102,
Myotis lucifugus	ENSMLUG00000009735	1 retrocopy	retro_mluc_1054,
Otolemur garnettii	ENSOGAG00000000895	1 retrocopy	retro_ogar_515,
Sus scrofa	ENSSSCG00000007322	5 retrocopies	retro_sscr_1116, retro_sscr_144, retro_sscr_519 , retro_sscr_539, retro_sscr_937,
Ictidomys tridecemlineatus	ENSSTOG00000022531	1 retrocopy	retro_itri_1284,