RetrogeneDB ID: retro_sscr_1150

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:36762595..36763394(+)
• Located in intron of: ENSSSCG00000027777

Retrocopy information

• Ensembl ID: ENSSSCG00000030880
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZNF259
• Ensembl ID: ENSSSCG00000015066
• Aliases: None
• Description: zinc finger protein 259 [Source:HGNC Symbol;Acc:13051]

Sequence

>retro_sscr_1150
CAAGTGGCCTTCCCTTTCACCCTGGCCGTTGATGATCCCTCAGGGAAGAGCCTTGTGGAAAACCCACATGCTCCCTGGAA
AGATGATACCCTGGTGATCACACACTGTAATCGCACTACAGCAGGAAGAGATCTGTGGCTCTGGGCAGAGGCGCCACAAG
AGGAAAATCTCAGAAACGAAGTGCTCCAGTTCAGCACAAACTGCCTGGAGTACCCTGTTCTGGCCCAGACCGACCTGAAG
CTAGTTGGAATCCCCCGTTTAAGGAGGTTATCATCATGGCTACCAACTGCAAGAATTGTAGCCATTGGACCAATGAGGTG
AAATCTGGAGGAGCCATAGAGCCCTTGGGCACCAGGATCACCCTCCACATCCCAGATCCTGAGATATGAGCAGAGACCTG
CTCCGGTTCAAGACATGTAGCATGGAAATCTTAGAGCAGGAATTTGAACTGGGAATGGCTGTCCTCAGGGGCAGGTTCAT
CACACTGGAGCGGATGCTGAAGCTTGTCTGGGAACTGGTGACCAGGAAACTTTTCACGCTGGGTGACAGTTCCATTCCTG
GCCAGGTGGAGAAACTGCAGGAGTTTAGCCAGAGGTTGGACCAGATCCCTGAGGGTAACATGAAGGCCCACTTTGTTATG
GATGATCCAGCTGGAAACAGCTACTTGCAGAATATACATACACCTGAAGATTATCCTGAGATGAAGGTAGAGCATTATAA
GTGCACATTTGACCCAAACGAGCAGCTAGGGCTCAACGGCATGAAGACGGAGGGCTATGAGACAGGCCTGGCTTCCCAG

Alignment

ORF - retro_sscr_1150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.71 %
• Parental protein coverage: 60.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVYSPFTLVIDDPSGNSFVENPHAPQKDESLEITRYSRTLQQEEMLGLRAGAPEEKPEEEDFRKEVLQFN
          .V..PFTL..DDPSG.S.VENPHAP.KD..L.IT...RT......L.L.A.AP.E....E..R.EVLQF.
Retrocopy QVAFPFTLAVDDPSGKSLVENPHAPWKDDTLVITHCNRTTAGRD-LWLWAEAPQE----ENLRNEVLQFS

Parental  TNCPECNAPAQTNMKLVQIPH-FKEVIIMATNCENCGHRTNEVKSGGAIEPLGTRITFHITDPS-DMTRD
          TNC.E....AQT..KLV.IP..FKEVIIMATNC.NC.H.TNEVKSGGAIEPLGTRIT.HI.DP..DM.RD
Retrocopy TNCLEYPVLAQTDLKLVGIPR<FKEVIIMATNCKNCSHWTNEVKSGGAIEPLGTRITLHIPDPE<DMSRD

Parental  LLKSETCSVEIPELEFELGMAVLGGKFTTLEGMLNDIRELVTKNPFTLGDSSNPGQAAKLQEFSQKLDQI
          LL...TCS.EI.E.EFELGMAVL.G.F.TLE.ML....ELVT...FTLGDSS.PGQ..KLQEFSQ.LDQI
Retrocopy LLRFKTCSMEILEQEFELGMAVLRGRFITLERMLKLVWELVTRKLFTLGDSSIPGQVEKLQEFSQRLDQI

Parental  LEGNMKAHFIMDDPAGNSYLQNVYAPEDDPEMKVEQYKRTFDQNEELGLNDMKTEGYETGLAAQ
          .EGNMKAHF.MDDPAGNSYLQN...PED.PEMKVE.YK.TFD.NE.LGLN.MKTEGYETGLA.Q
Retrocopy PEGNMKAHFVMDDPAGNSYLQNIHTPEDYPEMKVEHYKCTFDPNEQLGLNGMKTEGYETGLASQ

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	26.02 RPM
SRP014902_testis	0.14 RPM	77.09 RPM
SRP018288_heart	0.00 RPM	29.02 RPM
SRP018288_kidney	0.00 RPM	61.07 RPM
SRP018288_liver	0.00 RPM	394.18 RPM
SRP018288_lung	0.00 RPM	52.64 RPM
SRP018856_adipose	0.23 RPM	51.30 RPM
SRP035408_brain	0.00 RPM	83.82 RPM
SRP035408_liver	0.00 RPM	134.24 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1150 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1150 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011907	1 retrocopy	retro_etel_246,
Homo sapiens	ENSG00000109917	1 retrocopy	retro_hsap_3639,
Gorilla gorilla	ENSGGOG00000000664	1 retrocopy	retro_ggor_2455,
Myotis lucifugus	ENSMLUG00000014012	1 retrocopy	retro_mluc_2167,
Macaca mulatta	ENSMMUG00000020287	1 retrocopy	retro_mmul_1808,
Mus musculus	ENSMUSG00000032078	2 retrocopies	retro_mmus_3602, retro_mmus_3701,
Otolemur garnettii	ENSOGAG00000009977	1 retrocopy	retro_ogar_506,
Pongo abelii	ENSPPYG00000025914	1 retrocopy	retro_pabe_2986,
Pan troglodytes	ENSPTRG00000004312	1 retrocopy	retro_ptro_2464,
Sus scrofa	ENSSSCG00000015066	1 retrocopy	retro_sscr_1150 ,