RetrogeneDB ID: retro_sscr_349

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:162912415..162913187(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000002743
• Aliases: None
• Description: None

Sequence

>retro_sscr_349
ATTTTCACATCTGGATTTGGGGAGGAATAGTGCAGCATGCCAGACTCTGGATTTAAAGCTGAGCATTTTCTATTCAATTT
GAGATTAGTCATAAACCATCTTAAACTACTGGAGAAAAAAAAAAATGGAACTGGCACAGAGATCAAGGAAAGATATTGCT
GACTATCTGGCTCTTGGGAAAGATGAACAAGCTTGAATTCGAATGGAGCACCTTATTCGAGAAGACTATGTTGTGGAAGC
CATGGAGATCCTGGAGCTGTACTGTGAGCTGCTGCTGCTGGCTCAGTTTGTCCTCATCCAGTCTATGAAGGAGTTAGATT
CTAGTTTGGCTGAATCTGTGTCTATGATGATTTGGGCTGCTCCTCACCTCCAGTCAGAGGTGGCTGAGTTGAAAATAGTT
GCTGATCAACTTTGTGCTAAGTACAGCAAGGAATATGGCAAGTTATATAGGACCAACCAGATTGGAACTGTGAATGACAA
GCTAATGCACAAACTGAATGTGGAAGCCCCACCCAAAATGCAGGTGGAGAGATACCTGATTGAAATTGCCAAGAACTACA
ATGTGCCCTATGAGCCTGACTCTATGGTCATGGCAGAAGCTCCCCCTAGGGTACAGACATCTTATTGATGTTAGATTCAC
TGATGATGTGAAAAAGGGGGCTCTGCAGTAGGAGGCAGAGTTGGGTTGACAGCACCAGTTAGTGGACCTGATGGAACAGT
GCCAATGCCTATGCCATCTCCAAGTACTCCTTTGTCATACCCACTTCCAAAG

Alignment

ORF - retro_sscr_349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.23 %
• Parental protein coverage: 87.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFQLSVHEEQHSMLGSGFKAERLRVNLRLVINRLKLLEKKKT-ELAQKARKEIADYLAAGKDERARIRVE
          .F.....EE..SM..SGFKAE....NLRLVIN.LKLLE.....ELAQ..RK.IADYLA.GKDE.A.IR.E
Retrocopy IFTSGFGEE*CSMPDSGFKAEHFLFNLRLVINHLKLLEXXXX>ELAQRSRKDIADYLALGKDEQA*IRME

Parental  HIIREDYLVEAMEILELYCDLLL-ARFGLIQSMKELDSGLAESVSTLIWAAPRLQSEVAELKIVADQLCA
          H.IREDY.VEAMEILELYC.LLL.A.F.LIQSMKELDS.LAESVS..IWAAP.LQSEVAELKIVADQLCA
Retrocopy HLIREDYVVEAMEILELYCELLLLAQFVLIQSMKELDSSLAESVSMMIWAAPHLQSEVAELKIVADQLCA

Parental  KYSKEYGKLCRTNQIGTVNDRLMHKLSVEAPPKILVERYLIEIAKNYNVPYEPDSVVMAEA-PPGVETDL
          KYSKEYGKL.RTNQIGTVND.LMHKL.VEAPPK..VERYLIEIAKNYNVPYEPDS.VMAEA.P.G....L
Retrocopy KYSKEYGKLYRTNQIGTVNDKLMHKLNVEAPPKMQVERYLIEIAKNYNVPYEPDSMVMAEA>PLGYR-HL

Parental  IDVGFTDDVKKG-GSGRGGGGGFTAPVGGPDGTVPMPMPMPMPSPSTPFSYPLPK
          IDV.FTDDVKKG.GS..GG..G.TAPV.GPDGTVPMPMP.P....STP.SYPLPK
Retrocopy IDVRFTDDVKKG<GSAVGGRVGLTAPVSGPDGTVPMPMPSP----STPLSYPLPK

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	30.79 RPM
SRP014902_testis	0.00 RPM	42.29 RPM
SRP018288_heart	0.00 RPM	28.47 RPM
SRP018288_kidney	0.00 RPM	38.42 RPM
SRP018288_liver	0.00 RPM	23.03 RPM
SRP018288_lung	0.00 RPM	41.24 RPM
SRP018856_adipose	0.00 RPM	83.76 RPM
SRP035408_brain	0.00 RPM	22.11 RPM
SRP035408_liver	0.00 RPM	19.08 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_349 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_349 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015051	1 retrocopy	retro_cjac_1906,
Dipodomys ordii	ENSDORG00000002409	1 retrocopy	retro_dord_398,
Gorilla gorilla	ENSGGOG00000001863	1 retrocopy	retro_ggor_1446,
Mustela putorius furo	ENSMPUG00000007857	1 retrocopy	retro_mputfur_415,
Pongo abelii	ENSPPYG00000007522	1 retrocopy	retro_pabe_1695,
Sus scrofa	ENSSSCG00000002743	1 retrocopy	retro_sscr_349 ,