RetrogeneDB ID: retro_mmus_3543

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:150083752..150085295(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094767
• 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_3543
ATTACAGGATCCAAAGTCCAGCAGCTGAAGGTCAGTGTGGAGGACTCATACCCACTCAAGTACCATGTGGACATCTCATT
CACTCAGTTCACTCAAGAATACAGCCACCTGCAGCCTGGGGATCACCTGACTAACATCATAAGTGGCAGGTCACATCCAA
GAGAGTGTCTAGGGGAAAATTGATCTTCTATGACCTTCAAGGAGAGGAGGTCAAGTTACAAGTCATGGCCAACTCCAGGA
ATTATAAATCAGAGGAAGAATGTGTGCACCTCAATAAAAACTGCATCAGGGAGATATAATTAGAGTTGAGGGTAATCCAG
GGAAAACCAAGAAGGGCAAGTTGAGCACCATCCCCCAGGAGATCACACTTCTGTCCCTCTGCTTGCACATGTGCCTCAGC
TTCATTTTGGCCTTCAAAGACAAGGAAATAAGGTCTCTTCAGAGATATTTGGGCTTGATACTGAAGGAGTTTGTGAGATA
GAAATTTGTCATCTTTTCTAAAGATCATCACAGATATAAGAAGTTTCTTAGATGAGCTGGGATCCCTGAAATTTGGAACT
CCCATGATGAACATCATCCCTGGGAGAGCTTCAGCCGAGCCTTTCATCACCTATCACAATGAGCAGGAAAATGAACTTAT
GTATGAGAATTGCTCCAGAACTCTACCATAAGATGCTGGCTGTTGGTGCCATTGACAGGGTTTATGAAATTGGGCACCAG
TTCTGGAGTGAAGGGATTGATTTGACTCACATTCTGAATTCACCACCTGTGAGTTCTACATGGTCTATGCAGACAATAAT
GACCTTATGGAAATCACAGAGAAGATGCTGTCAGGGATAGTAGAAAGCATTACCAGCAGTTACAAGATCACCTGCCACCC
AGACAGACCAGAAGTGAAAGCCTGTGAAACTTACTTCACTCCACCCTTCAGAAGAGTCTGCATGGTAGAAGTGTTTGAGA
AAGCCCTAGGTATGAAGCTGCCAGAAACCAGTCTTTTTGAAATGGAAGAAACTTGAAACATTCTTGATATTTCTGTTGCA
AAAGCTGTTGAATGCCCCCCACCTAGGACCACAGCCAAGCTCCTTGATAAGCTTGTTGGAACATTCCTCGAAGTGACATG
CATCAGTCCTACATTCTTCTGTGATCACCCACAGATTATGAGTCCTTAGGCCAAATGGCACCACTCCAAAGAGGATTTAA
CTGAGCATTTTGAGCTGTTTGTCCTGAGAAGGATGTATGTGATGCCTACACTAAGCTGAATGATCCCATATGGCAGCAAT
AACAGTTTGAAGAGCAATCCAAGACCCAGTCTGCTGGTGATGATGATTCCATGTTCATAGATGAAAACTTCTGTGCTGCC
CTGGAATATGGGTTGCCCCCAACGGCTGGCTGGGGCATGGGTATGGATCAACTCAACCTGTTTCTCACAGATTCCATCAA
AATCAAGGGAGTACTTCTGTTTCCTACCATGAAGCCTAAAGACAAGAAGAAAACTGCAACAGCCACTGATACCCCAGAAA
GCACAGAGGCCAGCCCCTCTGTC

Alignment

ORF - retro_mmus_3543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.95 %
• Parental protein coverage: 83.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  IRSQAVQQLKVTGEDPYPHKFHVDISLTQFIQEYSHLQPGDHLTDVTLKVAGRIH-AKRASGGKLIFYDL
          I....VQQLKV..ED.YP.K.HVDIS.TQF.QEYSHLQPGDHLT.......GR.H..KR.S.GKLIFYDL
Retrocopy ITGSKVQQLKVSVEDSYPLKYHVDISFTQFTQEYSHLQPGDHLTNI---ISGRSH<SKRVSRGKLIFYDL

Parental  RGEGVKLQVMANSRNYKSEEEFVHINN-KLRRGDIIGVEGNPGKTKKGELSIIPQEITLLSPCLHM-LPH
          .GE.VKLQVMANSRNYKSEEE.VH.N..KL..GDII.VEGNPGKTKKG.LS.IPQEITLLS.CLHM..P.
Retrocopy QGEEVKLQVMANSRNYKSEEECVHLNK<KLHQGDIIRVEGNPGKTKKGKLSTIPQEITLLSLCLHM<VPQ

Parental  LHFGL-KDKETRYRQRYLDLILNDFVRQKFIVRSK-IITYIRSFLDELGFLEIETPMMNIIPGGAVAKPF
          LHFGL.KDKE.R..QRYL.LIL..FVR.KF...SK.IIT.IRSFLDELG.L...TPMMNIIPG.A.A.PF
Retrocopy LHFGL>KDKEIRSLQRYLGLILKEFVR*KFVIFSK>IITDIRSFLDELGSLKFGTPMMNIIPGRASAEPF

Parental  ITYHNELD-MNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTH-NPEFTTCEFYMAYADYHDLM
          ITYHNE...MNL.MRIAPELYHKML.VG.IDRVYEIG.QF..EGIDLTH...EFTTCEFYM.YAD..DLM
Retrocopy ITYHNEQE>MNLCMRIAPELYHKMLAVGAIDRVYEIGHQFWSEGIDLTH<HSEFTTCEFYMVYADNNDLM

Parental  EITEKMLSGMVKSITGSYKITYHPDGPEGQAYEVDFTPPFRRISMVEELEKALGVKLPETSLFETEETRK
          EITEKMLSG.V.SIT.SYKIT.HPD.PE..A.E..FTPPFRR..MVE..EKALG.KLPETSLFE.EET..
Retrocopy EITEKMLSGIVESITSSYKITCHPDRPEVKACETYFTPPFRRVCMVEVFEKALGMKLPETSLFEMEET*N

Parental  ILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCISPTFICDHPQIMSPLAKWHRSKEGLTERFELFVM
          ILD.I.VAKAVECPPPRTTA.LLDKLVG.FLEVTCISPTF.CDHPQIMSP.AKWH.SKE.LTE.FELFV.
Retrocopy ILD-ISVAKAVECPPPRTTAKLLDKLVGTFLEVTCISPTFFCDHPQIMSP*AKWHHSKEDLTEHFELFVL

Parental  K-KEICNAYTELNDPVRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRLTMFLTD
          ..K..C.AYT.LNDP..Q...FEEQ.K...AGDD..MFIDENFC.ALEYGLPPTAGWGMG.D.L..FLTD
Retrocopy R<KDVCDAYTKLNDPIWQQ*QFEEQSKTQSAGDDDSMFIDENFCAALEYGLPPTAGWGMGMDQLNLFLTD

Parental  SNNIKEVLLFPAMKPEDKKETAATTETPESTEASPSV
          S..IK.VLLFP.MKP.DKK.TA..T.TPESTEASPSV
Retrocopy SIKIKGVLLFPTMKPKDKKKTATATDTPESTEASPSV

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 activity near the 5' end of retro_mmus_3543 was not detected

EST

No EST(s) were mapped for retro_mmus_3543 retrocopy.

TSS

No TSS is located nearby retro_mmus_3543 retrocopy 5' end.

Lab

retro_mmus_3543 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3543 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,