RetrogeneDB ID: retro_sscr_549

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:46545957..46547216(-)
• Located in intron of: ENSSSCG00000029340

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDH1
• Ensembl ID: ENSSSCG00000023264
• Aliases: None
• Description: isocitrate dehydrogenase 1 (NADP+), soluble [Source:HGNC Symbol;Acc:5382]

Sequence

>retro_sscr_549
AGGTCTATCAAAGTTAAAATGTCTCAAGAAATCCAAGGTGGTTCTGTGGTAGAGATGCAAAAAGATGAAATGACTCGAAT
TATTTGGGAATTGATTAAAGAGAAACTCATTTTTCCCTACATGGAATTGGACCTGCAAGCTATGACTTAAGCATAGAGAA
TCGTGATGCCACCAATGACCAGGTCACCAAAGATGCTGCAGAAGCTGTAAAGAAATACAGTGCTGGTGTCAAGTGTGCCA
CCATCACCCCCAATGAGAAGAGAGTGGAGGAGTTCAAGTTGAAACAAATGTGGAAATTACAAAATGGCACCATCTGAAAT
ATCCTGGGTGGCACTGTCTTTTGGGAAGCTATTATCTGCAAAAATATTCCTTGGCTTGTGAGTGGCTGGGTAAAACCCAT
CATCATAGGTCATCATGCTTACAGGGATCAATACAGAGCAACACATTTTGTTGCTCCTGGGCCTGGAAAAGTAGAGATAT
CCTACACACCAAGCAATGGATCCCCCAAAATGACATATGTGGTACATGACTTCACAGACTGTTGTGGTGTTGTTATGTGG
ATGTACAATCAAGATAAGTCAGTCGAAGATTTTGCATACAGTTCTTTCCAGATGGATCTGTCCAAGAGTTGGCCCCTGTA
TCTGAGCACTAAAAATACTATCCTGAAGAAATATGATGGACATTTTAAAGACATCTTTCAGGAGATATATGACAAGCAGT
AGAAGTCTCAGTTTGAAGCTCAGAAGATCTGATATGGGCACCGGCTCATTGATTACATGGTGGCCCAAGCTACAAAATCA
GAGGGAAGCTTCATCTGGACCTGTAAAAACTATGATGGCAAAGTGCAGTCGGACTCCATGGCCCAAGGTTATGGCTCTCT
TGGCATGATGACCAGTGTGCTGGTTTGTCCAGATGGCAGGACAGTAGAAGCTGAGGCTGCCCACGAGACTGTAACACGTC
ACTACCATATGTACCAGAAAGGACAGGAGATGTCCACCAATGCCATTGCTTCCAGTTTTGCCTGGACCAGAGGGCTAGCC
CACAGAGCTAATTCTGATAACAATAAAGAGCTCAGCATCTTTGCAAAGGCTTTGAAAGAAGTCTGTATTGAGACTGTTGA
GGCTGGCTTCATGACCAAGGACTTGGCTGCTTGTGTTAAAGGTTTACCCAACGTGCAACATTCTGACTACTTGGATACAT
TTGAGTTCATGGACAAACTCAGAGAAAACTTGAAAATAAAACTAGCACAGGCCAAACTC

Alignment

ORF - retro_sscr_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.22 %
• Parental protein coverage: 98.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RFIKAKMSQKIQGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLH-SYDLGIENRDATNDQVTKDAAEA
          R.IK.KMSQ.IQGGSVVEMQ.DEMTRIIWELIKEKLIFPY.ELDL..SYDL.IENRDATNDQVTKDAAEA
Retrocopy RSIKVKMSQEIQGGSVVEMQKDEMTRIIWELIKEKLIFPYMELDLQ<SYDLSIENRDATNDQVTKDAAEA

Parental  IKKYNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGRH
          .KKY..GVKCATITP.EKRVEEFKLKQMWK..NGTI.NILGGTVF.EAIICKNIP.LVSGWVKPIIIG.H
Retrocopy VKKYSAGVKCATITPNEKRVEEFKLKQMWKLQNGTI*NILGGTVFWEAIICKNIPWLVSGWVKPIIIGHH

Parental  AYGDQYRATDFVVPGPGKVEISYTPRDGSPKMTYMVHDFTDCGGVAMGMYNQDKSIEDFAHSSFQMALSK
          AY.DQYRAT.FV.PGPGKVEISYTP..GSPKMTY.VHDFTDC.GV.M.MYNQDKS.EDFA.SSFQM.LSK
Retrocopy AYRDQYRATHFVAPGPGKVEISYTPSNGSPKMTYVVHDFTDCCGVVMWMYNQDKSVEDFAYSSFQMDLSK

Parental  GWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYD
          .WPLYLSTKNTILKKYDG.FKDIFQEIYDKQ.KSQFEAQKI.Y.HRLID.MVAQA.KSEG.FIW.CKNYD
Retrocopy SWPLYLSTKNTILKKYDGHFKDIFQEIYDKQ*KSQFEAQKI*YGHRLIDYMVAQATKSEGSFIWTCKNYD

Parental  GDVQSDSVAQGYGSLGMMTSVLICPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHR
          G.VQSDS.AQGYGSLGMMTSVL.CPDG.TVEAEAAH.TVTRHY.MYQKGQE.STN.IAS.FAWTRGLAHR
Retrocopy GKVQSDSMAQGYGSLGMMTSVLVCPDGRTVEAEAAHETVTRHYHMYQKGQEMSTNAIASSFAWTRGLAHR

Parental  AKLDSNKELSIFANALEEVCIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAK
          A..D.NKELSIFA.AL.EVCIET.EAGFMTKDLAAC.KGLPNVQ.SDYL.TFEFMDKL.ENLKIKLAQAK
Retrocopy ANSDNNKELSIFAKALKEVCIETVEAGFMTKDLAACVKGLPNVQHSDYLDTFEFMDKLRENLKIKLAQAK

Parental  L
          L
Retrocopy L

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	24.56 RPM
SRP014902_testis	0.57 RPM	87.56 RPM
SRP018288_heart	0.10 RPM	34.21 RPM
SRP018288_kidney	0.10 RPM	253.45 RPM
SRP018288_liver	0.16 RPM	405.53 RPM
SRP018288_lung	0.10 RPM	63.64 RPM
SRP018856_adipose	0.03 RPM	433.37 RPM
SRP035408_brain	0.19 RPM	55.36 RPM
SRP035408_liver	0.21 RPM	511.70 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_549 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_549 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020527	1 retrocopy	retro_btau_1235,
Choloepus hoffmanni	ENSCHOG00000004574	2 retrocopies	retro_chof_2158, retro_chof_897,
Cavia porcellus	ENSCPOG00000013587	1 retrocopy	retro_cpor_1010,
Homo sapiens	ENSG00000138413	1 retrocopy	retro_hsap_3554,
Gorilla gorilla	ENSGGOG00000012619	1 retrocopy	retro_ggor_2400,
Microcebus murinus	ENSMICG00000009797	1 retrocopy	retro_mmur_1364,
Macaca mulatta	ENSMMUG00000016077	1 retrocopy	retro_mmul_1817,
Nomascus leucogenys	ENSNLEG00000007143	3 retrocopies	retro_nleu_1169, retro_nleu_2328, retro_nleu_3117,
Otolemur garnettii	ENSOGAG00000014848	4 retrocopies	retro_ogar_1488, retro_ogar_2270, retro_ogar_2925, retro_ogar_3057,
Pongo abelii	ENSPPYG00000013125	2 retrocopies	retro_pabe_2935, retro_pabe_926,
Pan troglodytes	ENSPTRG00000012865	1 retrocopy	retro_ptro_2415,
Sus scrofa	ENSSSCG00000023264	1 retrocopy	retro_sscr_549 ,