RetrogeneDB ID: retro_ptro_268

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:221324558..221325758(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSPTRG00000022819
• Aliases: BECN1, beclin-1
• Description: None

Sequence

>retro_ptro_268
CCGGCGCCCACCTCCGGGCAGGCTGAGCCCGGAGACACCCGGGAGCCCGGCGTCACCACCAGGGAGGTGACAGACGCTGA
GGAGCAACAGGACGGTGCCTCTAGCAGACCCCTTCCAGGCGATGGCAGTGTGTCCAAGGACCATGCCAACATCTTCACCC
TGCTGGGGGAGCTTGGCGCCATGCACATGCTCAGTAGCATCCAGAAGGCAGCTGGTGACATTTTTGACATGGTCTCTGGC
CAAGCAGTTGTGGACCATCCCCTGTGTGAAGAATGCACCGACAGTCTTTTAGAGCAGCTGGACATCCAGCTCGCTCTCAC
AGAAGCTGACAGTCAGAACTACCAACGCTGCCTGGAGACCGGGGAGCTGGCGACCAGCGAGGACGAGACGGCGGCGCTGC
GGGCGGAGCTGCGGGACCTGGAGCTGGAGGAGGCCAGGCTGGTGCAGGAGCTGGAGGATGTGGACAGGAACAATGCAAGA
GCAGCGGCGCATCTCGAGGCAGCCCAGGCAGAGGCTGCGGAGCTGGACCAGCAGGAGAGGCAGCACTACAGGGACTACAG
TGCCTTGAAGTGGCAGCAGCTGGAACTGCTTGACCAGCTGGGGCACGTGGAGAACCAGCTGCAATATGCCAGGGTCCAGA
TGGACCGGCTGAAGGAAATCAACTGTTTCACCGCCACGTTTGAGATCTGGGTGGAGGGCCCCTTGGGCGTCATCAATAAC
TTCAGGTTGGGCCGCCTCCCCACTGTCCGTGTGGGCTGGAATGAGATTAACACTGCCTGGGGACAGGCGGCTTTGCTGCT
CCTTGCCCTGGCCAATACAATTGGACTGCAGTTTCAGAGGTATCGACTCATCCCCTGCGGAAACCATTCGTATCTGAAGT
CTCTAACAGATGACCGCGCTGAGCTGCCGTTGTTCTGTTATGGGGGGCAGGATGTTTTCCTCGATAACAAGTATGACCGC
GCGATGGTGGCCTTCCTGGACTGCATGCAGCAGTTCAAGGAAGAGGCTGAGAAGGGTGAGCTGGGCCTCTCTCTGCCCTA
CGGGATCCAGGTGGAGACAGGGCTGATGGAGGACGTTGGCGGCCGAGGGGAATGCTATTCCATCAGAACCCATCTGAACA
CGCAGGAGCTGTGGACAAAGGCACTCAAGTTCATGCTCATAAATTTCAAGTGGAGTCTCATCTGGGTTGCCTCAAGGTAT

Alignment

ORF - retro_ptro_268 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.92 %
• Parental protein coverage: 89.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLLTTAQAKPGETQEEETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSR
          P..T..QA.PG.T.E......E....E...QDG.S.R..P.....S...AN.FTL.GE....G.M..LS.
Retrocopy PAPTSGQAEPGDTREPGVTTREVTDAEE-QQDGASSRPLPGDGSVSKDHANIFTLLGEL---GAMHMLSS

Parental  RLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILE-QMNEDDSEQLQME
          ..K..GD.FD..SGQ..VDHPLCEECTD.LL.QLD.QL..TE...QNY.RCLE..E....ED....L..E
Retrocopy IQKAAGDIFDMVSGQAVVDHPLCEECTDSLLEQLDIQLALTEADSQNYQRCLETGELATSEDETAALRAE

Parental  LKELALEEERLIQELEDVEKNRKTVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVENQ
          L..L.LEE.RL.QELEDV..N....A..LE..QAEA..LDQ.E.Q..R.YS..K.QQLEL.D.L..VENQ
Retrocopy LRDLELEEARLVQELEDVDRNNARAAAHLEAAQAEAAELDQQERQHYRDYSALKWQQLELLDQLGHVENQ

Parental  MRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMGL
          ..YA..Q.D.LK..N.F.ATF.IW..G..G.INNFRLGRLP.V.V.WNEIN.AWGQ..LLL.ALAN..GL
Retrocopy LQYARVQMDRLKEINCFTATFEIWVEGPLGVINNFRLGRLPTVRVGWNEINTAWGQAALLLLALANTIGL

Parental  KFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLP
          .FQRYRL.P.GNHSYL.SLTD...ELPL.C.GG...F.DNK.D.AMVAFLDC.QQFKEE.EKGE....LP
Retrocopy QFQRYRLIPCGNHSYLKSLTDDRAELPLFCYGGQDVFLDNKYDRAMVAFLDCMQQFKEEAEKGELGLSLP

Parental  YRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQF
          Y...VE.G..ED.GG.G..YSI.T..N..E.WTKALKFML.N.KW.L.WV.S..
Retrocopy YGIQVETGLMEDVGGRGECYSIRTHLNTQELWTKALKFMLINFKWSLIWVASRY

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
SRP007412_brain_prefrontal_cortex	0.05 RPM	31.33 RPM
SRP007412_cerebellum	0.00 RPM	59.33 RPM
SRP007412_heart	0.00 RPM	43.69 RPM
SRP007412_kidney	0.00 RPM	47.07 RPM
SRP007412_liver	0.00 RPM	32.41 RPM
SRP007412_testis	0.00 RPM	29.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_268 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_268 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_268 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_81

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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,