RetrogeneDB ID: retro_sscr_818

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:46008538..46009408(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G6PD
• Ensembl ID: ENSSSCG00000025108
• Aliases: None
• Description: glucose-6-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4057]

Sequence

>retro_sscr_818
GCATCAATGACAGAACAGGTGGCTCTGAGCCAGCCCCAGGTGTGCGGGATCCTGAGGGAAGAGCTGTACCAACACGATTC
CTTTCATCAGTCTGAGATACATATCTTCATTATCATGGGCGCATCCGGCAACCTGGCCAAGAAGATCTACCCCACCGTTT
GCTGGCTTTTCCAGGATGGCCTTCTGCTGGAAGATACCTTCATCATAGGCTCCGCCCACTCCCGCCTCACAGTGGCTGAC
ATCCACATGTGGAGCAAACTGTTCATCAAAGCTACCCCAGAGGAGAAGCCCAAGCTGGAGGAGTTCTTTGCCCGCAACTC
CTACATGGCTGGCCAATAGGATGACGTGGCCTCCTGTGAGCACCTCAACAGCCACCTGAATCCTTTCCACCACAGTCCGC
AAGCCAACTGCCTCTTCTACCTGGCTTTGCCCCCCTCTGTCTACGAGGCTGTCACCAAGAACATCCATGAGACCTGCATG
AGCCAGATAGGCTGGAACCGTATCATTGTGGAGAAGCCTTTTAGGAGGGACTTGCAGAGTTCCAACTAGCTGTCCAACCA
CATTTCCTCCCTGTTTCAAAAGGACCAGATCTACCACATCAACCACTACCTGGGCAAGGAGATGGTCCAGAACCTCATGG
TGCTGAGGTTTGCCAACAGGATCTTCAGCCCCATCTGGAACTGTGACAACATCACTTGCGTCATCCTCACCTTCAAGGAG
CCCTTTGGCACTGAGGGCCATGGAGGCTACTTCAGTGAGTTTGGGATCATCCAGGATGTGATGCAGAATCACATCCTGCA
AGTGCTGTGTCTGGTGGCCATGGAGAAGCTCACTTCCACCAACTCAGATGACATCTGTAATGAGAAGGTC

Alignment

ORF - retro_sscr_818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.32 %
• Parental protein coverage: 56.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STMAEQVALSRTQVCGILREELYQGDAFHQSDTHIFIIMGASGDLAKKKIYPTLWWLFRDGLLPEDTYIV
          ..M.EQVALS..QVCGILREELYQ.D.FHQS..HIFIIMGASG.LAKK.IYPT..WLF.DGLL.EDT.I.
Retrocopy ASMTEQVALSQPQVCGILREELYQHDSFHQSEIHIFIIMGASGNLAKK-IYPTVCWLFQDGLLLEDTFII

Parental  GYARSRLSVADIRRQSEPFFKATPEEKPRLEEFFARNSYVAGQYDDAASYARLNSHMNALHQGSQANRLF
          G.A.SRL.VADI...S..F.KATPEEKP.LEEFFARNSY.AGQ.DD.AS...LNSH.N..H...QAN.LF
Retrocopy GSAHSRLTVADIHMWSKLFIKATPEEKPKLEEFFARNSYMAGQ*DDVASCEHLNSHLNPFHHSPQANCLF

Parental  YLALPPTVYEAVTKNIRETCMSRAGWNRVIVEKPFGRDLQSSDQLSNHISSLFREDQIYRIDHYLGKEMV
          YLALPP.VYEAVTKNI.ETCMS..GWNR.IVEKPF.RDLQSS..LSNHISSLF..DQIY.I.HYLGKEMV
Retrocopy YLALPPSVYEAVTKNIHETCMSQIGWNRIIVEKPFRRDLQSSN*LSNHISSLFQKDQIYHINHYLGKEMV

Parental  QNLMVLRFANRIFGPIWNRDNIACVILTFKEPFGTEGRGGYFDEFGIIRDVMQNHLLQMLCLVAMEKPAS
          QNLMVLRFANRIF.PIWN.DNI.CVILTFKEPFGTEG.GGYF.EFGII.DVMQNH.LQ.LCLVAMEK..S
Retrocopy QNLMVLRFANRIFSPIWNCDNITCVILTFKEPFGTEGHGGYFSEFGIIQDVMQNHILQVLCLVAMEKLTS

Parental  TDSDDVRDEKV
          T.SDD...EKV
Retrocopy TNSDDICNEKV

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	696.17 RPM
SRP014902_testis	0.28 RPM	90.38 RPM
SRP018288_heart	0.16 RPM	8.22 RPM
SRP018288_kidney	0.10 RPM	28.07 RPM
SRP018288_liver	0.16 RPM	9.91 RPM
SRP018288_lung	0.00 RPM	106.51 RPM
SRP018856_adipose	0.00 RPM	61.49 RPM
SRP035408_brain	0.00 RPM	51.74 RPM
SRP035408_liver	0.06 RPM	12.59 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_818 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_818 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_818 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016775	2 retrocopies	retro_cjac_4026, retro_cjac_499,
Equus caballus	ENSECAG00000014994	1 retrocopy	retro_ecab_492,
Myotis lucifugus	ENSMLUG00000008210	1 retrocopy	retro_mluc_842,
Mus musculus	ENSMUSG00000031400	1 retrocopy	retro_mmus_174,
Sus scrofa	ENSSSCG00000025108	1 retrocopy	retro_sscr_818 ,