RetrogeneDB ID: retro_sscr_357

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:193086140..193086805(+)
• Located in intron of: ENSSSCG00000012019

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1D
• Ensembl ID: ENSSSCG00000002288
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D [Source:HGNC Symbol;Acc:13527]

Sequence

>retro_sscr_357
ATGTCGGGCAAAGACTGAATTGAAATCTTTCTCTTGAGAATGGCACAGATCATCATGAAAGCTCAGTTAAAAGGAGCAGA
CAGGTCAAAAGCTCGGAAGAAAAAACTCTGATGCCTTAACCCTTTGATTTCCACTGATCCTTAAGAAGATAATAGAGACT
AAAATGCTGATGGGTGAAGTGATGAGAGAAGCTGCTTTTTCACTTGCTGAGGCCAAGTTCACAGCAGGGACTTCAACACC
ACAGTTATCCAAGATATAAATAAAGCCCAAATGAAGATTAGAGCAAAGAAGATAACATAGCAGTGTTACCTTGCCAGTAT
TTGAACATAATCATGAAGGAACTGACAGTTATTAGCTGACTGCTTTAGCCAAAGGTGGCGAACAGTTGGCTAAACTGAAG
AAGGATTATGCCAAAGCAGTAAAACTAGCGGAGGAACCAGATTTGCTGCAGACTTTTGTTACTTTGGATGAAGCTATTAA
GATAACCAACAGGTGTGTAAATGTCATTGAACATGTCATCATTCCCCAGATTGAATGCACCCTCGATTATAGCGTCACAG
GGTTGGATGAGAGCGAGAAGAGTTCTATAGGTTAAAGAAAATACAAGAGAAGAAAAAGATTCTCAGGGAAAATCTGAGAA
GAACTTGGAGCAACGGAAGGCAGCT

Alignment

ORF - retro_sscr_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.41 %
• Parental protein coverage: 91.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKK-SDALTLRFRQILKKIIETKMLMGEVMREAAFSL
          MSGKD.IEIF..RMAQ.IMKA.LKGA.......KKK.SDALTL.F..ILKKIIETKMLMGEVMREAAFSL
Retrocopy MSGKD*IEIFLLRMAQIIMKAQLKGADRSK-ARKKK>SDALTL*FPLILKKIIETKMLMGEVMREAAFSL

Parental  AEAKFTAG-DFSTTVIQNVNKAQVKIRAKK-DNVA-GVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKR
          AEAKFTAG.DF.TTVIQ..NKAQ.KIRAKK.DN.A..VTLPVFEH.HEGTDSY.LT.LA.GGEQLAKLK.
Retrocopy AEAKFTAG<DFNTTVIQDINKAQMKIRAKK<DNIA<SVTLPVFEHNHEGTDSY*LTALAKGGEQLAKLKK

Parental  NYAKAVELLVELASLQTSFVTLDEAIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQ
          .YAKAV.L..E...LQT.FVTLDEAIKITNR.VN.IEHVIIP.IE.TL.Y..T.LDE.E........K..
Retrocopy DYAKAVKLAEEPDLLQT-FVTLDEAIKITNRCVNVIEHVIIPQIECTLDYSVTGLDESEKSSI-G*RKYK

Parental  EKK-KILKE-KSEKDLEQRRAA
          ..K.KIL.E.KSEK.LEQR.AA
Retrocopy RRK<KILRE<KSEKNLEQRKAA

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	16.19 RPM
SRP014902_testis	0.00 RPM	28.01 RPM
SRP018288_heart	0.00 RPM	21.74 RPM
SRP018288_kidney	0.00 RPM	129.63 RPM
SRP018288_liver	0.00 RPM	21.91 RPM
SRP018288_lung	0.00 RPM	30.45 RPM
SRP018856_adipose	0.00 RPM	20.18 RPM
SRP035408_brain	0.00 RPM	87.98 RPM
SRP035408_liver	0.03 RPM	30.62 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_357 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_357 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008240	1 retrocopy	retro_amel_332,
Bos taurus	ENSBTAG00000016309	2 retrocopies	retro_btau_1757, retro_btau_408,
Canis familiaris	ENSCAFG00000016369	2 retrocopies	retro_cfam_1186, retro_cfam_999,
Choloepus hoffmanni	ENSCHOG00000003733	5 retrocopies	retro_chof_1229, retro_chof_2711, retro_chof_54, retro_chof_926, retro_chof_938,
Cavia porcellus	ENSCPOG00000009085	1 retrocopy	retro_cpor_36,
Felis catus	ENSFCAG00000011078	1 retrocopy	retro_fcat_632,
Myotis lucifugus	ENSMLUG00000006244	5 retrocopies	retro_mluc_2345, retro_mluc_442, retro_mluc_540, retro_mluc_666, retro_mluc_94,
Macaca mulatta	ENSMMUG00000021418	1 retrocopy	retro_mmul_1159,
Monodelphis domestica	ENSMODG00000009896	5 retrocopies	retro_mdom_1196, retro_mdom_1522, retro_mdom_1730, retro_mdom_390, retro_mdom_594,
Mustela putorius furo	ENSMPUG00000007002	2 retrocopies	retro_mputfur_1381, retro_mputfur_748,
Otolemur garnettii	ENSOGAG00000015052	1 retrocopy	retro_ogar_966,
Sus scrofa	ENSSSCG00000002288	1 retrocopy	retro_sscr_357 ,
Ictidomys tridecemlineatus	ENSSTOG00000027710	1 retrocopy	retro_itri_383,
Vicugna pacos	ENSVPAG00000005696	1 retrocopy	retro_vpac_232,
Drosophila melanogaster	FBgn0040377	1 retrocopy	retro_dmel_70,