RetrogeneDB ID: retro_mmus_2729

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:43373804..43375318(+)
• Located in intron of: ENSMUSG00000029735

Retrocopy information

• Ensembl ID: ENSMUSG00000084325
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atic
• Ensembl ID: ENSMUSG00000026192
• Aliases: Atic, 2610509C24Rik, AA536954, AW212393
• Description: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase [Source:MGI Symbol;Acc:MGI:1351352]

Sequence

>retro_mmus_2729
ATGGCTCCCTCTCAGCTTGCCCTGTTCAGTGTGTCTGACAAAACTGGCCTTGTGGAATTTGCCAGAAACCTTGAATCTCT
TGGCTTGAGTCTGGTTACTTCTGGGGGCACAGCAAAAGCTATCAGGGATGCTGGCCTGTCAGTCAGAGATGTGTCTGAGC
TAACGGGGTTCCTGAAAATGTTAGGGGTGTGTGTGAAAACCTTGCATCTTGCCATCCGTGCTGGAATCTTGGCATTCAAT
ATTCCTGAAGATACTGCTGACATGGCCAGGCTTGATAACCTTCTAAGAGTTGTTGTCTGTAACCTGTATCCCTTTGTGAA
GACTGTAGCTTCTCCAGATGTAACTGTTGAGACAGCTATTGAGCAAACTGATATTGGTGGCATGACCTTACTGAGAGCTG
TAGCCAAAAACCATGCTCGAGTGACAGTCATCTGTGAACCAGAGGATTATGTGGCAGTGGCTGCAGAGATGCAGGGCTCT
GATAGTAAGGACACTTCCCTGGAGACCAGGCGCCATGTGGTGTTGAACGCATTCTCCCATACCGCTCAATATGATGAAGC
AAATTCAGATTACTCCTAGAAACAGTACAGTAAAGGAATTTCTCAGATGTCCCTGAGGTATGGGATGAGCCACCATCAGA
CTCCTTCCCAGCTGTATACACTGAAGCCCAAGCTACCCATCACAGCTCTCAATGGAGCCCCGGGATTCATAAACTTGTGT
GATACTTTGAAGGCCTGGCAGCTGGTGACAGAACTGAGAGGAGCAGTAGACATTCCAGCTGGGGCTTCTTTCAAGCTTGT
CAGCCCAGCAGGTGTTGCTGTTGGGGTTCCACTCAGTGAGGACAAGGCCAGAGTTTGCATGGTCTATGACCTCTATCCGA
CTTTTATGCTCCTGGCCATTGCATATTCAAGAGCAAGAGGAGCAGAGAGGATGTCTTCATTTGGTTATTTTGTTGCATTA
TCTGACATTAGTGATGTCCAAATTGCAAAAATTATCTCCAGAGAAGTGTCAGATGGTATTGTTGCCCTGGGATATGAAGA
AGACTTGAAAATACTTTTTAAAAAGAAACTGTAAACTACTTTGTTCTTCAAATGGATCAGTCATACAAACCAGATGAAAA
TGAAGTTCGAACACTCTTTGGTCTTCGTTTAAGCCAGAAGAGAAATAATGGTGTCATTGACATGTCGTTATTTAGCAATA
TTATCACCAAGAATAAAGATCTGCTGGAGTCTGCTCTCAGAGACCTCATTGTCGCCACATTAGCTGTCAAGTATACTCAG
TCTAATTTGGTGTGTTATGCCAAGGACAGGCAGGTTATTGGCATCGGAGTAGGACAACAGCCTTGGATACAGTGCACATG
CCTTGCAGATGATAAGGGTAACTCTTGGTGGGTTTGATACCACCCACAAGTGCTTTCCATGAAGTTTAAAGCTGGGGTGA
AGATAGCAGAAATCTCCAATTCCATTGATGAGTATGTAACCAGCACCATTGGTGAGGATGAAGACCTGGTGAAA

Alignment

ORF - retro_mmus_2729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.66 %
• Parental protein coverage: 85.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSQLALFSVSDKTGLVEFARSLASLGLSLVASGGTAKAIRDAGLAVRDVSELTGFPEMLGGRVKTLHP
          MAPSQLALFSVSDKTGLVEFAR.L.SLGLSLV.SGGTAKAIRDAGL.VRDVSELTGF..MLG..VKTLH.
Retrocopy MAPSQLALFSVSDKTGLVEFARNLESLGLSLVTSGGTAKAIRDAGLSVRDVSELTGFLKMLGVCVKTLHL

Parental  AVHAGILARNIPEDAADMARLDFNLVRVVVCNLYPFVKTVASPDVTVEAAVEQIDIGGVTLLRAAAKNHA
          A..AGILA.NIPED.ADMARLD.NL.RVVVCNLYPFVKTVASPDVTVE.A.EQ.DIGG.TLLRA.AKNHA
Retrocopy AIRAGILAFNIPEDTADMARLD-NLLRVVVCNLYPFVKTVASPDVTVETAIEQTDIGGMTLLRAVAKNHA

Parental  RVTVVCEPEDYAGVAAEMHGSDSKDTSLETRRHLALKAFTHTAQYDEAISDYFRKQYSKGISQMPLRYGM
          RVTV.CEPEDY..VAAEM.GSDSKDTSLETRRH..L.AF.HTAQYDEA.SDY..KQYSKGISQM.LRYGM
Retrocopy RVTVICEPEDYVAVAAEMQGSDSKDTSLETRRHVVLNAFSHTAQYDEANSDYS*KQYSKGISQMSLRYGM

Parental  NPHQTPAQLYTLKPKLPITVLNGAPGFINLCDALNAWQLVTELRGAVDIPAAASFKHVSPAGAAVGVPLS
          ..HQTP.QLYTLKPKLPIT.LNGAPGFINLCD.L.AWQLVTELRGAVDIPA.ASFK.VSPAG.AVGVPLS
Retrocopy SHHQTPSQLYTLKPKLPITALNGAPGFINLCDTLKAWQLVTELRGAVDIPAGASFKLVSPAGVAVGVPLS

Parental  EDEARVCMVYDLYPTLTPLAVAYARARGADRMSSFGDFVALSDICDVPTAKIISREVSDGIVAPGYEEEA
          ED.ARVCMVYDLYPT...LA.AY.RARGA.RMSSFG.FVALSDI.DV..AKIISREVSDGIVA.GYEE..
Retrocopy EDKARVCMVYDLYPTFMLLAIAYSRARGAERMSSFGYFVALSDISDVQIAKIISREVSDGIVALGYEED-

Parental  LKILSKKK-NGNYCVLQMDQSYKPDENEVRTLFGLRLSQKRNNGVVDKSLFSNIVTKNKDLPESALRDLI
          LKIL.KKK...NY.VLQMDQSYKPDENEVRTLFGLRLSQKRNNGV.D.SLFSNI.TKNKDL.ESALRDLI
Retrocopy LKILFKKK<TVNYFVLQMDQSYKPDENEVRTLFGLRLSQKRNNGVIDMSLFSNIITKNKDLLESALRDLI

Parental  VATVAVKYTQSNSVCYAKDGQVIGIGAGQQSRIHCTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEISN
          VAT.AVKYTQSN.VCYAKD.QVIGIG.GQQ..I.CT.LA.DK.NSWW...HP.VLSMKFKAGVK.AEISN
Retrocopy VATLAVKYTQSNLVCYAKDRQVIGIGVGQQPWIQCTCLADDKGNSWWV*YHPQVLSMKFKAGVKIAEISN

Parental  AIDQYVTGTIGEGEDLVK
          .ID.YVT.TIGE.EDLVK
Retrocopy SIDEYVTSTIGEDEDLVK

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	0.05 RPM	27.69 RPM
SRP007412_cerebellum	0.00 RPM	35.87 RPM
SRP007412_heart	0.09 RPM	31.88 RPM
SRP007412_kidney	0.02 RPM	49.84 RPM
SRP007412_liver	0.03 RPM	40.31 RPM
SRP007412_testis	0.00 RPM	17.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2729 was not detected

EST

No EST(s) were mapped for retro_mmus_2729 retrocopy.

TSS

No TSS is located nearby retro_mmus_2729 retrocopy 5' end.

Lab

retro_mmus_2729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2729 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011695	4 retrocopies	retro_cjac_1538, retro_cjac_2185, retro_cjac_3116, retro_cjac_706,
Microcebus murinus	ENSMICG00000014573	1 retrocopy	retro_mmur_1591,
Myotis lucifugus	ENSMLUG00000001830	1 retrocopy	retro_mluc_1370,
Monodelphis domestica	ENSMODG00000015612	1 retrocopy	retro_mdom_1074,
Mustela putorius furo	ENSMPUG00000007676	1 retrocopy	retro_mputfur_1609,
Mus musculus	ENSMUSG00000026192	1 retrocopy	retro_mmus_2729 ,
Rattus norvegicus	ENSRNOG00000015511	1 retrocopy	retro_rnor_904,