RetrogeneDB ID: retro_sscr_939

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 7:62820129..62820989(-)
• Located in intron of: ENSSSCG00000001878

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHN2
• Ensembl ID: ENSSSCG00000016687
• Aliases: None
• Description: chimerin 2 [Source:HGNC Symbol;Acc:1944]

Sequence

>retro_sscr_939
GAAAGCCAGTGTCAGCCAGGAACCTATACTTTAGCTTTCAGATTTGGAAGTCAAACCAGATACTTCAGGCTCTACTATGA
TGGAAAGCACTTCACTGGGGAGAAGAGCTTTGAGTCCATCCATGATCTGATGACTGATGGATTGATTGTTCTCTATATTG
ATATTGAAACTAAGTCAGCAGGATACATTGCCAAAATCATGAGAAACCCAATTTCTGAGCACACAGGACACACAACCTTA
AACAGAGGGCCAGCACAGCAAAAACATACGCCAGTCCTGAAAGAGACACATGATGAGAAAGACTCTATAGGCCAGGATGG
CGTATCAGAGAAAAGGTTGACAGCACTTGTTAGAAGAGCAACTCTGAAAGAAAATGAGCAAATTCCAAGACAGGTTCACA
GTTTCAGAGTCCATAAATACAGAGGGCCACACTGGTATGAATACTATGCCAGCTTCATGTTAGGGCTCATTGCTTAGGGA
GTGAAATGTACAGATTGTGGTTTGAATGTTTATAAGCAGTGTTACAACATGGTCCCAAATGACTGTAAGCCAGACTTGAA
ACATGTCAAGAAGGTGTACAGTTGTGACCTTATGACATTTGCAAAAGCCTACACCGCTAAGCAGGCCATGGTGGTGGACA
TATGCATCAAGGAAACTGAATCTCGAGATTTTAATTCTGAAGGACTGCATGGTATATCAGGATTTAGTGACCTAATTAAA
GATGTCAAGATGGTTTTTGACAGAGATGATGAGAAAGCAGGTATTTCTGTGAACGTGTGTGAAGATTCAACATTATCACT
GGTGTGCTAAAACTGTACTTCAGGGATTTACCAATCGCACTTATCACATATGATGCCTAC

Alignment

ORF - retro_sscr_939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.9 %
• Parental protein coverage: 68.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESQRQPGCYTLALRFGNQTLNYRLFYDGKHFVGEKRFESIHDLVTDGLITLYI--ETKASEYISKMTTNP
          ESQ.QPG.YTLA.RFG.QT...RL.YDGKHF.GEK.FESIHDL.TDGLI.LYI..ETK...YI.K...NP
Retrocopy ESQCQPGTYTLAFRFGSQTRYFRLYYDGKHFTGEKSFESIHDLMTDGLIVLYIDIETKSAGYIAKIMRNP

Parental  IYEHIGYATLLREKVSRRLSRSKNESR-KANVTNEEHAAVEKISSLVRRAALTHHDNHFNYEKTHNFKVH
          I.EH.G..TL.R............E....................LVRRA.L....N.......H.F.VH
Retrocopy ISEHTGHTTLNRGPAQQKHTPVLKETHDEKDSIGQDGVSEKRLTALVRRATLK--ENEQIPRQVHSFRVH

Parental  TFRGPHWCEYCANFMWGLIAQGVRCSDCGLNVHKQCSKHVPNDCQPDLKRIKKVYCCDLTTLVKAHNTQR
          ..RGPHW.EY.A.FM.GLIA.GV.C.DCGLNV.KQC...VPNDC.PDLK..KKVY.CDL.T..KA.....
Retrocopy KYRGPHWYEYYASFMLGLIA*GVKCTDCGLNVYKQCYNMVPNDCKPDLKHVKKVYSCDLMTFAKAYTAKQ

Parental  PMVVDICIREIEARGLKSEGLYRVSGFTEHIEDVKMAFDRDGEKADISASIYPD-INIITGALKLYFRDL
          .MVVDICI.E.E.R...SEGL...SGF...I.DVKM.FDRD.EKA.IS.....D..NIITG.LKLYFRDL
Retrocopy AMVVDICIKETESRDFNSEGLHGISGFSDLIKDVKMVFDRDDEKAGISVNVCED<FNIITGVLKLYFRDL

Parental  PIPVITYDTY
          PI..ITYD.Y
Retrocopy PIALITYDAY

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	0.40 RPM
SRP014902_testis	0.42 RPM	3.39 RPM
SRP018288_heart	0.08 RPM	6.68 RPM
SRP018288_kidney	0.00 RPM	1.28 RPM
SRP018288_liver	0.00 RPM	21.91 RPM
SRP018288_lung	0.10 RPM	8.86 RPM
SRP018856_adipose	0.00 RPM	1.26 RPM
SRP035408_brain	3.81 RPM	8.13 RPM
SRP035408_liver	0.00 RPM	22.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_939 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003023	1 retrocopy	retro_cfam_2185,
Macaca mulatta	ENSMMUG00000008329	1 retrocopy	retro_mmul_1926,
Oryctolagus cuniculus	ENSOCUG00000009401	1 retrocopy	retro_ocun_440,
Sus scrofa	ENSSSCG00000016687	1 retrocopy	retro_sscr_939 ,