RetrogeneDB ID: retro_dord_675

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_51342:4948..6013(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000007211
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Becn1
• Ensembl ID: ENSDORG00000000956
• Aliases: None
• Description: beclin 1, autophagy related [Source:MGI Symbol;Acc:MGI:1891828]

Sequence

>retro_dord_675
TTCACCCTGCTTGGGAATGCTGTGTCCCTCCGAACTCTGAGCAGCATCCAGAAGACCCTGGTGGACATCTTTGCCATCCT
GTCGGGCCGGAAAGTGGTGGAGCACCCGCTGTGCCAGGAGTGTACTGACCATCTTCTGGAGCAGGTGGATGCTCGGCTCT
CGCAGGCGGAGCTGGACTGCCAGGCCTACCGACGTGCCCTGGAGACGGAGTTGCTGGTGGATCCGGAGGACAGGAGGGCC
CTGGACAGCCGGCTGCGGGCAGAGCTGCGGGAGCTGGAGCGGGCGGAGGCCCGGCTGACGGAGGAGCTGGCCGACGCCGA
GCAGGCCTGGGCCCAAGCGGCCCACGACCTGCAGGCGTCCCAGGCAGAGACGGCCGAGCTGCACCAGCAGGCCGCGCAGT
ACCGGAAGGAATACTGCGCCCTGGAGTGGCAACGGCTCGAACTGACGGACCAGCTGAGCAGCGTGGAGAACCAGCTGCGG
TCCGCCCGGGGCCAGCTGGACAAGCTGAGCACCACCAGCATCTTCGATGTCACCTTCCAGATCTGGGAGGAGGGCCCCCT
GGGCGTCATCAATAACTTCAGGCTGGGCTACCTGCCCCGCGTCCCCGTGAGCTGGACGGAGATCAGCGCTGCCTGGGGAC
AGGCGGCCTTGCTGCTCCTCGCCCTCGCCAATACCATTGGACTCAAGTTTCGGAGGTACCAACTCGTGGCCGGTGGAAAC
CATTCCTATCTGAAGTCGCTGACGGGTGACGGTGTCCGCCTGCCCTTGTTCTCCGATGGGAAGCAGAATGTCTTCTTGGA
AAACACATTTGATCGCGCCATGATGGCTTTCCTGGATTGCATGCAACAGTTCAAGGAAGAGGCAGAGAAGGGCCGGGGGG
GCTTGTACCTTCCCTACAGCATGCATCCGGAGCTGGGCACGCTAGAGGATGCCAAGGGCAGCGGGGAGTGGTACTCCATC
CGGACCCACCTCAACACAGTGGAAGAGTGGACACGGGCTCTCAAATTCCTGCTTGTCAATTTAAAGTGGAGTCTTGCTTG
GGCCTCAGAAAGGTACAGTCAAAAA

Alignment

ORF - retro_dord_675 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.56 %
• Parental protein coverage: 79.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKCCL
          FTL.G.A....T.......L....D.F.I.SG...V.HPLC.ECTD.LL.Q.D..L...E..CQ.Y...L
Retrocopy FTLLGNAVSLRTLSSIQKTLV---DIFAILSGRKVVEHPLCQECTDHLLEQVDARLSQAELDCQAYRRAL

Parental  EILEQVNEDD----SEQLQRELRELVLEEERLIQELEDVEKNRKVVAENLEKVQAXXXXXXXXXXXYQRE
          E....V...D.......L..ELREL...E.RL..EL.D.E......A..L...QA...........Y..E
Retrocopy ETELLVDPEDRRALDSRLRAELRELERAEARLTEELADAEQAWAQAAHDLQASQAETAELHQQAAQYRKE

Parental  YSEFKRQQLELDDELKSVENQMRYAQIQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNE
          Y.....Q.LEL.D.L.SVENQ.R.A..QLDKL..T..F..TF.IW..G..G.INNFRLG.LP.VPV.W.E
Retrocopy YCALEWQRLELTDQLSSVENQLRSARGQLDKLSTTSIFDVTFQIWEEGPLGVINNFRLGYLPRVPVSWTE

Parental  INAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAF
          I.AAWGQ..LLL.ALAN..GLKF.RY.LV..GNHSYL.SLT.....LPL...G....F..N.FD.AM.AF
Retrocopy ISAAWGQAALLLLALANTIGLKFRRYQLVAGGNHSYLKSLTGDGVRLPLFSDGKQNVFLENTFDRAMMAF

Parental  LDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAW
          LDC.QQFKEE.EKG.....LPY.M..E.G..ED..GSG..YSI.T..N..E.WT.ALKF.L.NLKW.LAW
Retrocopy LDCMQQFKEEAEKGRGGLYLPYSMHPELGTLEDAKGSGEWYSIRTHLNTVEEWTRALKFLLVNLKWSLAW

Parental  VSSQFYNK
          .S.....K
Retrocopy ASERYSQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_675 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,