RetrogeneDB ID: retro_sscr_511

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:122690610..122691141(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016142
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BNIP3L
• Ensembl ID: ENSSSCG00000009658
• Aliases: None
• Description: BCL2/adenovirus E1B 19kDa interacting protein 3-like [Source:HGNC Symbol;Acc:1085]

Sequence

>retro_sscr_511
TCTCACTTATTAGAGCAGCTGCCACCTCTGCCCAACAACCACCACCGTGAGAAAAGGCAGGCAGCCTCTGCCCCCACCAG
CCAACCTCAACGTTCCTGGTGGAGCGCCCCATGCAGAGCAGCCAGGGCAATGGGGAAGATGGGGGCTAGGACGTGCACCG
TCCTCATCCTCTACCCGCAGTGGAGACACAGAGAAGATTCTTCTGGATGAACAACATGAATCTGGACAGAGAAGTTCAAG
AGGCAGCTTCCACTGTGATGGCGATTTCCCACAAGAGGATGGGTGGATCATGTTTGATGTGGAAAATACACACCAGCAGG
GACCACAGCCCTCAGTCAGAGAAGAGCTTGTAGGAGGAGGGAAAGAAGAGGATGCTGTGAAGAAAAGTGTAGACTGGGTG
TCCGCCTGGCCTAGCAGACCTGAAACATTCCACCTCAGGAGCTCCACTTCGGGCACCCTAAACGTTGTTTCTTTAAGCAT
GAGCAAAGGTGGAACCATGAAGAGAAGGGGGAGTTCCTGCAGTGTTCATTC

Alignment

ORF - retro_sscr_511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.58 %
• Parental protein coverage: 83.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  SHLVEQPPPLHNNNNNCEE-GEQSLPPPAGLN-SSW-VELPMNSSNGNDNGNGKNGG-LEHVPSSSSIHN
          SHL.EQ.PPL.N.N...E..G.Q.LPPPA.LN..SW.VE.PM.SS.....GNG..GG.L...PSSSS...
Retrocopy SHLLEQLPPLPN-NHHREK>GRQPLPPPANLN<RSW<VERPMQSSQ----GNGEDGG<LGRAPSSSSTRS

Parental  GDMEKILLDAQHESGQSSSRGSSHCDSPSPQEDGQIMFDVE-MHTSRDHSSQSE-EEVVEGEKEVDALKK
          GD.EKILLD.QHESGQ.SSRGS.HCD...PQEDG.IMFDVE..HTSRDHS.QSE.EE.V.G.KE.DA.KK
Retrocopy GDTEKILLDEQHESGQRSSRGSFHCDGDFPQEDGWIMFDVE>IHTSRDHSPQSE<EELVGGGKEEDAVKK

Parental  SVDWVSDWSSRPE-NIPPKEFHFRHPKRSVSLSMRKSGAMKKGGIFSAEF
          SVDWVS.W.SRPE.NIPP.E.HF.HPKR.............KG......F
Retrocopy SVDWVSAWPSRPE<NIPPQELHFGHPKRCFFKHEQRWNHEEKGEFLQCSF

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	54.02 RPM
SRP014902_testis	0.00 RPM	64.22 RPM
SRP018288_heart	0.00 RPM	40.10 RPM
SRP018288_kidney	0.00 RPM	58.32 RPM
SRP018288_liver	0.00 RPM	42.86 RPM
SRP018288_lung	0.00 RPM	118.32 RPM
SRP018856_adipose	0.08 RPM	125.84 RPM
SRP035408_brain	0.00 RPM	97.31 RPM
SRP035408_liver	0.00 RPM	28.39 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_511 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_511 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021307	4 retrocopies	retro_btau_1148, retro_btau_1170, retro_btau_1790, retro_btau_449,
Choloepus hoffmanni	ENSCHOG00000007732	3 retrocopies	retro_chof_2356, retro_chof_2475, retro_chof_980,
Dasypus novemcinctus	ENSDNOG00000016179	1 retrocopy	retro_dnov_2101,
Dipodomys ordii	ENSDORG00000009336	1 retrocopy	retro_dord_169,
Erinaceus europaeus	ENSEEUG00000006302	1 retrocopy	retro_eeur_269,
Echinops telfairi	ENSETEG00000012037	3 retrocopies	retro_etel_1178, retro_etel_1428, retro_etel_603,
Felis catus	ENSFCAG00000030159	2 retrocopies	retro_fcat_616, retro_fcat_944,
Macropus eugenii	ENSMEUG00000011173	1 retrocopy	retro_meug_962,
Myotis lucifugus	ENSMLUG00000014949	1 retrocopy	retro_mluc_2192,
Mustela putorius furo	ENSMPUG00000000829	1 retrocopy	retro_mputfur_297,
Mus musculus	ENSMUSG00000022051	2 retrocopies	retro_mmus_482, retro_mmus_849,
Oryctolagus cuniculus	ENSOCUG00000010542	1 retrocopy	retro_ocun_1460,
Otolemur garnettii	ENSOGAG00000003163	2 retrocopies	retro_ogar_1039, retro_ogar_2651,
Ochotona princeps	ENSOPRG00000016284	1 retrocopy	retro_opri_1105,
Rattus norvegicus	ENSRNOG00000009820	1 retrocopy	retro_rnor_1183,
Sus scrofa	ENSSSCG00000009658	1 retrocopy	retro_sscr_511 ,
Sus scrofa	ENSSSCG00000024388	1 retrocopy	retro_sscr_827,
Ictidomys tridecemlineatus	ENSSTOG00000004029	1 retrocopy	retro_itri_1525,
Tupaia belangeri	ENSTBEG00000006361	2 retrocopies	retro_tbel_3371, retro_tbel_4006,
Tarsius syrichta	ENSTSYG00000011036	4 retrocopies	retro_tsyr_1182, retro_tsyr_1602, retro_tsyr_162, retro_tsyr_1997,
Tursiops truncatus	ENSTTRG00000004862	1 retrocopy	retro_ttru_725,
Vicugna pacos	ENSVPAG00000000509	2 retrocopies	retro_vpac_349, retro_vpac_534,