RetrogeneDB ID: retro_sscr_75

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:17717265..17718576(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000010868
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSSSCG00000017386
• Aliases: BECN1, ATG6
• Description: beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]

Sequence

>retro_sscr_75
AGCGCCGGGGTGAGAGTCAAGACCGCCGCCATGTCCTCCTTCCGCTTCATCTGCCAGCGCTGCAGCCAGCCCCTGAAACT
GACAGAGTCCACGGAAACCTCCCAGGAACGTGCAGCTTCGTTGCTCCACTCTGCTCGAGGGGAGCCAGGAGAACCCCAGG
GGGCTTCTTCCGGAGAGGGAGCCAGTGTCATAAATCTACAGGATGGCGCCTCTTGCCTGCCCTTCCCTGGTGGCGGGATG
TTCTGGGCCAGTTCTGAATTCACTCTGCTTGGGAGACTGGGCTCCCTGAGAAGCCTCAACAGCATCCAGAAGGCCATTAG
GGACATTTTTGGCATCCTCTCCGGTGAAACGGTTGTGGATCACCCCCTCTGCCAGCACTGTACTGACTGTCTTTTAGAGC
AACTGGATGCTCAACTCACCACGACAGATTCTGAGGTTCAGAACTACAGGCGCTGTTTAGAGACCAGGGGGTGGGGGAGT
GAGGCTGAGAGGGAGACGCTGCGGAAGCAGCTGAAGGGCCTGGAGCTGGAGGAATTGAGGCTGGTCCAAGAGCTGGAGCA
GGTGCAGAAGAACCGAGAAAGGACCACAGCAGATCTGGAGGCAGCCCAGGCGGAGACTGAGATGCTGGACCAGAAGGAAT
GGCAGTACCAGAAAGACTACAGTAAGTTGAAATGGCAGCAACTAGAACTTCACGACGAGCTGGACAGTGTGGCGAGGCGG
CTAGAGCACGCCCAGACCCGGTGGGACCAGCTGGAGAAAACCAATGTCTTCAGGGCCACATTTGAGATCAGGCATGCTGG
TCCTATAGCCATCATCAATAACTTCAGGCTGGGCTCCCTCCCCACGGTCCCTGTGGGCTGGAATGAGATAAACGCAGCCT
GGGGACAGACTGCCTTGCTGCTCCACGCCCTGTCCAACGCAATTGGCCTGGAGTTTCAGAGGTATCGACTTGTCCCCTGC
GGAAACTACTCCTACCTGAAGTCTTTAACAGGTGACCACGTTGAGCTGCCATTATTTGCAAATGGGCAGCAGAGTGTTTT
CTTGAATAACAAATTCGACCAGGCGATGGTGGCTTTCCTGGACTGCATGCAGCAGTTCAAGGAAGCAGCTGAGAAAAGTG
AGCCACCACTCTTTTGGCCCTACAAGATTGACGTGAAGAAAGGCCTGATGGAAGACCCTGGAAGCCATGGTGGATTCTGT
CCCATCAGGACCCACCTGAACACAGAGGAGGAGTGGACGCGAGCGCTCAAGCTCATGCTTATAAATTTTAAGTCGAGTCT
CCTGTGGGTCTCCTTAAGGTATCGTCAAAAA

Alignment

ORF - retro_sscr_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.13 %
• Parental protein coverage: 91.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIQELTAPLLATAQVKPGETQEEEANPGEEPFIETRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGT
          T.QE..A.LL..A...PGE.Q...A..GE.......QDG.S....P...M....S...FTL.G.....G.
Retrocopy TSQERAASLLHSARGEPGEPQG--ASSGEGASVINLQDGASCLPFPGGGMFWASS--EFTLLGRL---GS

Parental  MENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMHEDDSE
          ...L....K...D.F.I.SG.T.VDHPLC..CTD.LL.QLD.QL..T..E.QNY.RCLE......E...E
Retrocopy LRSLNSIQKAIRDIFGILSGETVVDHPLCQHCTDCLLEQLDAQLTTTDSEVQNYRRCLETRGWGSEAERE

Parental  QLRMELRELALEEERLIQELEEVEKNRIIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELK
          .LR..L..L.LEE.RL.QELE.V.KNR......LE..QAE.E.LDQ.E.QYQ..YS..K.QQLEL.DEL.
Retrocopy TLRKQLKGLELEELRLVQELEQVQKNRERTTADLEAAQAETEMLDQKEWQYQKDYSKLKWQQLELHDELD

Parental  SVENQMRYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALA
          SV......AQ...D.L.KTNVF.ATF.I.H.G....INNFRLG.LP.VPV.WNEINAAWGQT.LLLHAL.
Retrocopy SVARRLEHAQTRWDQLEKTNVFRATFEIRHAGPIAIINNFRLGSLPTVPVGWNEINAAWGQTALLLHALS

Parental  NKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGET
          N..GL.FQRYRLVP.GN.SYL.SLT....ELPL...G....F..NKFD.AMVAFLDC.QQFKE..EK.E.
Retrocopy NAIGLEFQRYRLVPCGNYSYLKSLTGDHVELPLFANGQQSVFLNNKFDQAMVAFLDCMQQFKEAAEKSEP

Parental  RFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK
          ....PY..DV.KG..ED.G..GG...I.T..N.EE.WT.ALK.ML.N.K..L.WVS.....K
Retrocopy PLFWPYKIDVKKGLMEDPGSHGGFCPIRTHLNTEEEWTRALKLMLINFKSSLLWVSLRYRQK

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	28.01 RPM
SRP014902_testis	0.00 RPM	29.99 RPM
SRP018288_heart	0.00 RPM	45.52 RPM
SRP018288_kidney	0.00 RPM	73.09 RPM
SRP018288_liver	0.00 RPM	27.66 RPM
SRP018288_lung	0.10 RPM	65.27 RPM
SRP018856_adipose	0.00 RPM	100.00 RPM
SRP035408_brain	0.06 RPM	114.85 RPM
SRP035408_liver	0.00 RPM	36.87 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_75 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_75 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_75 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75 ,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,