RetrogeneDB ID: retro_mmus_3541

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:149380640..149382182(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095408
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Kars
• Ensembl ID: ENSMUSG00000031948
• Aliases: Kars, AA589550, AL024334, AL033315, AL033367, D8Ertd698e, D8Wsu108e, LysRS, mKIAA0070
• Description: lysyl-tRNA synthetase [Source:MGI Symbol;Acc:MGI:1934754]

Sequence

>retro_mmus_3541
ATTACAGGATCCAAAGTCCAGCAGCTGAAGGTCAGTGTGGAGGACTCATACCCACTCAAGTACCATGTGGACATCTCATT
CACTCAGTTCACTCAAGAATACAGCCACCTGCAGCCTGGGGATCACCTGACTAACAACATAAGTGGCAGGTCACATCCAA
GAGAGTGTCTGGGGAAAATTCATCTTCTATGACCTTTGAGGAGAGGAGGTCAAGTTACAAGTCATGGCCAACTCCAGGAA
TTATAAATCAGAGGAAGAATGTGTGCATCTCAATAAAAACTGCATCAGGGAGATATAATTAGAGTTGAGGGTAATCCAGG
GAAAACCAAGAAGGGCAAGCTGAGCACCATCCCCCAGGAGATCACACTTCTGTCCCTCTGCTTGCACATGTGCCTCAGCT
TCATTTTGGCCTTCAAAGACAAGGAAATAAGGTCTCTTCAGAGATATTTGGGCTTGATACTGAAGGAGTTTGTGAGATAG
AAATTTGTCATCTTCTCTAAAGATAATCACAGATATAAGAAGTTTCTTAGATGAGCTGGGATCCCTGGACTTTGGAACTC
CCATGATGAGCATCATCCCTGGGGGAGCTTCAGCCAAGCCTTTCATCACCTATCACAATGAGCAGGAAAATGAACTTATG
TATGAGAATTGCTCCAGAACCCTACCATAAGATGCTGGCTGTTGGTGCCATTGACAGGGTTTATGAAATTGGGCACCAGT
TCTGGAGTGAAGGGATTGATTTGACTCACATTCTGAATTCACCACCTGTGAGTTCTACATGGTCTATGCAGACAGTCATG
ACCTCATGGAAATCACAGAGAAGATGCTGTCAGGGATGGTAGAAAGCATTACCAGCAGTTACAAGATCACCTGCCACCCA
GACAGGCCAGAAGTCCAAGCCTGTGAAACTTACTTCACTCCACCCTTCAGGAGAATCAGCATGGTAGAAGTGTTTGAGAA
AGCCCTAGGTATGAAGCTGCCAGAAACCAGTCTCTTTGAAATAGAAGAAACTTGAAAAATTCTTGATATTTCTGTTGCAA
AAGCTGTTGAATGCTCCCCACCTAGGACCACAGCCAAGCTCCTTGATAAGCTTGTTGGAACATTCCTCGAAGTGACATGC
ATCAGTCCTACATTCTTCTGTGATCACCCACAGATTATGAGTCCTTAGACCAAATGGCACCACTCCAAAGAGGATTTAAC
TGAGCATTTTGAGCTGTTTGTCCTGAGAAGGATGTATGTGATGCCTACACTAAGCTGAATGATCCCATATGGCAGCAATA
ACAGTTTGAAGAGCAATCCAAGACCCAGTCTGCTGGTGATGATGATTCCATGTTCATAGATGAAAACTTCTGTGCTGCCC
TGGAATATGGGTTGCCCCCAACGGCTGGCTGGGGCATGGGTATGGATCAACTCAACCTGTTTCTCACAGATTCCATCAAA
ATCAAGGGAGTACTTCTGTTTCCTACCATGAAGCCTAAAGACAAGAAGAAAACTGCAACAGCCACTGATACCCCAGAAAG
CACAGAGGCCAGCCCCTCTGTC

Alignment

ORF - retro_mmus_3541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.57 %
• Parental protein coverage: 87.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  IRSQAVQQLKVTGEDPYPHKFHVDISLTQFIQEYSHLQPGDHLTDVTLKVAGRIH-AKRASG-GKLIFYD
          I....VQQLKV..ED.YP.K.HVDIS.TQF.QEYSHLQPGDHLT.......GR.H..KR.SG.GK.IFYD
Retrocopy ITGSKVQQLKVSVEDSYPLKYHVDISFTQFTQEYSHLQPGDHLTN---NISGRSH<SKRVSG<GKFIFYD

Parental  LRGEGVKLQVMANSRNYKSEEEFVHINN-KLRRGDIIGVEGNPGKTKKGELSIIPQEITLLSPCLHM-LP
          L.GE.VKLQVMANSRNYKSEEE.VH.N..KL..GDII.VEGNPGKTKKG.LS.IPQEITLLS.CLHM..P
Retrocopy L*GEEVKLQVMANSRNYKSEEECVHLNK<KLHQGDIIRVEGNPGKTKKGKLSTIPQEITLLSLCLHM<VP

Parental  HLHFGL-KDKETRYRQRYLDLILNDFVRQKFIVRSK-IITYIRSFLDELGFLEIETPMMNIIPGGAVAKP
          .LHFGL.KDKE.R..QRYL.LIL..FVR.KF...SK.IIT.IRSFLDELG.L...TPMM.IIPGGA.AKP
Retrocopy QLHFGL>KDKEIRSLQRYLGLILKEFVR*KFVIFSK>IITDIRSFLDELGSLDFGTPMMSIIPGGASAKP

Parental  FITYHNELD-MNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTH-NPEFTTCEFYMAYADYHDL
          FITYHNE...MNL.MRIAPE.YHKML.VG.IDRVYEIG.QF..EGIDLTH...EFTTCEFYM.YAD.HDL
Retrocopy FITYHNEQE>MNLCMRIAPEPYHKMLAVGAIDRVYEIGHQFWSEGIDLTH<HSEFTTCEFYMVYADSHDL

Parental  MEITEKMLSGMVKSITGSYKITYHPDGPEGQAYEVDFTPPFRRISMVEELEKALGVKLPETSLFETEETR
          MEITEKMLSGMV.SIT.SYKIT.HPD.PE.QA.E..FTPPFRRISMVE..EKALG.KLPETSLFE.EET.
Retrocopy MEITEKMLSGMVESITSSYKITCHPDRPEVQACETYFTPPFRRISMVEVFEKALGMKLPETSLFEIEET*

Parental  KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCISPTFICDHPQIMSPLAKWHRSKEGLTERFELFV
          KILD.I.VAKAVEC.PPRTTA.LLDKLVG.FLEVTCISPTF.CDHPQIMSP..KWH.SKE.LTE.FELFV
Retrocopy KILD-ISVAKAVECSPPRTTAKLLDKLVGTFLEVTCISPTFFCDHPQIMSP*TKWHHSKEDLTEHFELFV

Parental  MK-KEICNAYTELNDPVRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRLTMFLT
          ...K..C.AYT.LNDP..Q...FEEQ.K...AGDD..MFIDENFC.ALEYGLPPTAGWGMG.D.L..FLT
Retrocopy LR<KDVCDAYTKLNDPIWQQ*QFEEQSKTQSAGDDDSMFIDENFCAALEYGLPPTAGWGMGMDQLNLFLT

Parental  DSNNIKEVLLFPAMKPEDKKETAATTETPESTEASPSV
          DS..IK.VLLFP.MKP.DKK.TA..T.TPESTEASPSV
Retrocopy DSIKIKGVLLFPTMKPKDKKKTATATDTPESTEASPSV

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	57.24 RPM
SRP007412_cerebellum	0.00 RPM	70.00 RPM
SRP007412_heart	0.00 RPM	104.38 RPM
SRP007412_kidney	0.00 RPM	86.62 RPM
SRP007412_liver	0.00 RPM	64.45 RPM
SRP007412_testis	0.00 RPM	100.26 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3541 was not detected

EST

No EST(s) were mapped for retro_mmus_3541 retrocopy.

TSS

No TSS is located nearby retro_mmus_3541 retrocopy 5' end.

Lab

retro_mmus_3541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013447	1 retrocopy	retro_chof_2324,
Callithrix jacchus	ENSCJAG00000014213	2 retrocopies	retro_cjac_4104, retro_cjac_608,
Homo sapiens	ENSG00000065427	1 retrocopy	retro_hsap_1191,
Gorilla gorilla	ENSGGOG00000005515	1 retrocopy	retro_ggor_930,
Mus musculus	ENSMUSG00000031948	8 retrocopies	retro_mmus_3536, retro_mmus_3537, retro_mmus_3538, retro_mmus_3539, retro_mmus_3540, retro_mmus_3541 , retro_mmus_3542, retro_mmus_3543,
Nomascus leucogenys	ENSNLEG00000013072	1 retrocopy	retro_nleu_2080,
Pongo abelii	ENSPPYG00000007567	1 retrocopy	retro_pabe_992,
Pan troglodytes	ENSPTRG00000008364	1 retrocopy	retro_ptro_3036,
Pteropus vampyrus	ENSPVAG00000006746	2 retrocopies	retro_pvam_1301, retro_pvam_723,
Sorex araneus	ENSSARG00000011493	1 retrocopy	retro_sara_415,