RetrogeneDB ID: retro_mmus_1503

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:23717168..23718754(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083681
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Abce1
• Ensembl ID: ENSMUSG00000058355
• Aliases: Abce1, C79080, Oabp, RLI, RNS41, Rnaseli
• Description: ATP-binding cassette, sub-family E (OABP), member 1 [Source:MGI Symbol;Acc:MGI:1195458]

Sequence

>retro_mmus_1503
ATGGCAGACAAATTAACAAGAATTGCTATTTTCAACCACAATAAATGCAAACCTAAGAAATGGAGGCAGGAGTGCAAAGA
GAGTTGCCCTGTGGTTCAGATGGGGAAATTATGCATCGAGGTTACACCCCAGAGCAAAATAGCATAGATTTCTGGAACTC
TTTGTATTGGTTATGGTATTTTTATTAAGAAATGTCCCTTTGGCGCCTTATCAATTGTCAATTTGCCAAGCAACTTGGAA
AAAGAAATAACACATTGCTATTGTGCCAATGCCTTCAAGCTTCACAGGTTGCCTATCCCTCCTCCAGGTGAAGTTTTGAG
ATTAGTTGGAATGAATGGTATTGGAAATTCAACTGCACTAAAAATTTTAGCAGGAAAACAAAAGTCAAACCTTGGAAAGT
ATGATGATCCGCCTAATTGGCAAGAGATCTTGGCTTATTTCCCTGGATCTGAATTACAAAATTACTTTACCAAGATTTTC
GAAGATGACCTAAAAGCCATTATCAAACCTCAATATGTAGACCAAATTCCCAAAGATGCAAAGGGGACAGTGGGCTCTAT
TCTGGACAGAAAAGATGAAACAAAGACACAGGCAAGAGTATGTCAGCAGCTTGATTTAACTCACCTTAAAGAACTAAATG
TCGAAGATCTTTCAGGAGGAGAGTTGCAGAGATTTGCTTGTGTTGTCATTTGCATACAAAAAGCTGATATTTTTATGTTT
GATGAACCTCCTTGTTACTTTGATGTCAAGCAGCATTTAAAGGCTGCCATTACTATTCTATCTCTAATAAATCCAGATAG
ATATATCATTGTGGTGGAGCATGATCTAAGTACATTAGACTATCTCTCTGACTTCATCTGTTGTCTATATAGTGTATCAA
GTGCTTATGGTGCTGTCACTATGACTTTTAGTGTAAGAGAAGGCATAAATATAGTTTTGGATGGCTATATTCCAACAGAG
AACTTGAGGTTCAGGGATGTGTTGCTTGTTTTTAAGGTAGCTGAGACAGCAAATGAAGAAGAAGTTAAAAAGATGTGCAT
GTACAAATATCTTGGGATGAAAAAAAAGATGGGAGAGTTCAAGCTCACAATTGTAGCTGGAGAGTTCACGGACTCTGAGA
TCATGGTGAGGCTGGGGGAGAATGGTATTGGTAAAACTACATTTATCAGAATGCCTGCTGGAAGGCTTAAACCAGATAAG
GAGAAGAAGTACCAGTTCTAAATGTCAGTTATAAGACACAGAAAATCAGTCCCAAATCAACAGTAAGTGTTCACCAGTGA
CTGCATGAAAGATCAGAGATGCTTAATACTCATCCGCAGTTTGTGACTGCAGTAATGAAGCCCCTACAGATTGAAAACAT
CATTGACCAAGAGGTACAGACATTGTCTGGTGGTGAACTTCATCGAGGAGCTTTAGCTCTTTGTTTGGGCAAGCCTGCTG
ACGTCTATTTAATCGAGGAAACTTCTGCATATTTGGATTTTGAGCAAAGATTAATGACAGCTCAGGTCGTCAAACATTTC
ATTCTCCGTGCAAAGAAGACAGCTTTTGTTGTAGAACATGACTTCATCATGGCCACCTACCTAGCA

Alignment

ORF - retro_mmus_1503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.6 %
• Parental protein coverage: 88.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGICIKKCPFGAL
          MADKLTRIAI.NH.KCKPKK.RQECK.SCPVV.MGKLCIEVTPQSKIA.IS.TLCIG.GI.IKKCPFGAL
Retrocopy MADKLTRIAIFNHNKCKPKKWRQECKESCPVVQMGKLCIEVTPQSKIA*ISGTLCIGYGIFIKKCPFGAL

Parental  SIVNLPSNLEKETTHRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTALKILAGKQKPNLGKYDDPPDW
          SIVNLPSNLEKE.TH.YCANAFKLHRLPIP.PGEVL.LVG.NGIG.STALKILAGKQK.NLGKYDDPP.W
Retrocopy SIVNLPSNLEKEITHCYCANAFKLHRLPIPPPGEVLRLVGMNGIGNSTALKILAGKQKSNLGKYDDPPNW

Parental  QEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQLDLTHLK
          QEIL.YF.GSELQNYFTKI.EDDLKAIIKPQYVDQIPK.AKGTVGSILDRKDETKTQA.VCQQLDLTHLK
Retrocopy QEILAYFPGSELQNYFTKIFEDDLKAIIKPQYVDQIPKDAKGTVGSILDRKDETKTQARVCQQLDLTHLK

Parental  ERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRLKAAITIRSLINPDRYIIVVEHDLSVLD
          E.NVEDLSGGELQRFAC.V.CIQKADIFMFDEP..Y.DVKQ.LKAAITI.SLINPDRYIIVVEHDLS.LD
Retrocopy ELNVEDLSGGELQRFACVVICIQKADIFMFDEPPCYFDVKQHLKAAITILSLINPDRYIIVVEHDLSTLD

Parental  YLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMCMYKY
          YLSDFICCLY.V.SAYG.VTM.FSVREGINI.LDGY.PTENLRFRD..LVFKVAETANEEEVKKMCMYKY
Retrocopy YLSDFICCLYSVSSAYGAVTMTFSVREGINIVLDGYIPTENLRFRDVLLVFKVAETANEEEVKKMCMYKY

Parental  PGMKKKMGEFELAIVAGEFTDSEIMVMLGENGTGKTTFIRMLAGRLKPDE-GGEVPVLNVSYKPQKISPK
          .GM...MGEF.L.IVAGEFTDSEIMV.LGENG.GKTTFIRM.AGRLKPD..G.EVPVLNVSYK.QKISPK
Retrocopy LGMXXXMGEFKLTIVAGEFTDSEIMVRLGENGIGKTTFIRMPAGRLKPDK<GEEVPVLNVSYKTQKISPK

Parental  STGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLIDEPS
          ST.SV.Q.LHE......THPQFVT.VMKPLQIENIIDQEVQTLSGGEL.R.ALALCLGKPADVYLI.E.S
Retrocopy STVSVHQ*LHERSEMLNTHPQFVTAVMKPLQIENIIDQEVQTLSGGELHRGALALCLGKPADVYLIEETS

Parental  AYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLA
          AYLD.EQRLM.A.VVK.FIL.AKKTAFVVEHDFIMATYLA
Retrocopy AYLDFEQRLMTAQVVKHFILRAKKTAFVVEHDFIMATYLA

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	0.00 RPM	83.29 RPM
SRP007412_cerebellum	0.00 RPM	70.86 RPM
SRP007412_heart	0.03 RPM	56.84 RPM
SRP007412_kidney	0.00 RPM	78.04 RPM
SRP007412_liver	0.00 RPM	74.06 RPM
SRP007412_testis	0.05 RPM	95.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1503 was not detected

EST

No EST(s) were mapped for retro_mmus_1503 retrocopy.

TSS

No TSS is located nearby retro_mmus_1503 retrocopy 5' end.

Lab

retro_mmus_1503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1503 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503 ,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925, retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603,