RetrogeneDB ID: retro_mmus_382

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:161746341..161747645(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Gpt
• Ensembl ID: ENSMUSG00000022546
• Aliases: Gpt, 1300007J06Rik, 2310022B03Rik, ALT, Gpt-1, Gpt1
• Description: glutamic pyruvic transaminase, soluble [Source:MGI Symbol;Acc:MGI:95802]

Sequence

>retro_mmus_382
ACTGAGGTAATCCGAGCCAACATTGGGGATGCCCATGCTATGGGCCAGCAGCCAATCACCTTCCTCCATCAGGTGATGGC
ACTCTGCACTTTCCCAAACCTGCTAAACAGCCCCAGCTTCCCAGAAGATGCTAAGAAAGGAGCCGGGCGGATCCTGCAGG
CTTGTGGTGGAAACAGCTTGGGATTTTACAGTGCTAGCCAGGGCTTTAACTGTACCTGTGAGGATATGGCAGCCTTTATC
ACCGGGAGAGATGGTGTGCCTGCAGACCCAGACAACATTTACCTGACTACTGGAGCTAGCGACGGTATTTCTACGATCCT
AAAGCTCCTGGTCTCCGGTGCTGGCAAGTCACGGACAGGCGAGATGATTCCCATCCCACAGTACCCCTTGTACTCTGCGG
TCATCTCCGAGCTCAACGCGGTTCAGGTGAACTACATTCTGGATGAGAACTGCTGGGCTTTAAATGTGGACGAGCTCCGG
CGGGCATTGCGGCAAGCCAAAGATCACTAAAGTGGCCCTAAAGTTCTCTTGCATTATCAACCCTGGAAACCCCACGAGCC
AGGTACAAAGCAGAAAGTGCAGAGAAGATGTGATTTGCTTTGCCTGAAAAGAGAAGCTTTTTCTCCTGGCTGATGAGCTA
TACCAGGACAACGTGTGCTCTCCAGACTGCAGATTCCACTCGTTTAAGAAAGTGCTTTACCAGATAGATGGGGCATGAGT
ACTCCAGCAATGTGGAGCTCGCCTCCTTCCACTCCACCTCCAAGGGCTACGTGGGCAAGTGTGACTACAGAGGGGGCTAC
ATGGAGGTGATCAGTTTGCACCCTGAGATCGAAGGCCAGCTGGTGAAGCTACTCTCCATTCGCCTCTGTCCGCCCGTGTC
TGGACAGGTCGCTATGGACATTGTTGTGAATCCACCAGTACCAGGAGAGGAGTCCTTTGAGCAATTCAGCAGAGAAAAAG
AATTCGTCCTTGGTAATCTGGCCAAAAAAGCAAAGCTGACAGAAGATCTGTTTAACCAAGTGCCAGGGATTCAGTGCGAC
CCCTTGCAAAGAGCCATGTATGCGTTTCCTCGGATTCTCATCCCTGCCAAGGCCGTGGAGGCGGCTCAGTCCCATAAAAT
GGCTCCAGACTTGGTTTACTACATGAAACTCTTGGAGGAGACTGGCATCTGTGTTGTGCCTGGCAGTGGCTTTGGACAGC
GAGAAGGCACTTACCACTTCAGAATGACAATTCTCCCTCCCGTGGAGAAACTGAAGACCCTGCTCCATAAGGTCTTTCAC
CTGAACTTCCTGGAGCAGTACTCC

Alignment

ORF - retro_mmus_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.95 %
• Parental protein coverage: 87.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TEVIRANIGDAQAMGQRPITFFRQVLALCVYPNLLSSPDFPEDAKRRAERILQACGGHSLGAYSISSGIQ
          TEVIRANIGDA.AMGQ.PITF..QV.ALC..PNLL.SP.FPEDAK..A.RILQACGG.SLG.YS.S.G..
Retrocopy TEVIRANIGDAHAMGQQPITFLHQVMALCTFPNLLNSPSFPEDAKKGAGRILQACGGNSLGFYSASQGFN

Parental  PIREDVAQYIERRDGGIPADPNNIFLSTGASDAIVTMLKLLVAGEGRARTGVLIPIPQYPLYSAALAELD
          ...ED.A..I..RDG..PADP.NI.L.TGASD.I.T.LKLLV.G.G..RTG..IPIPQYPLYSA...EL.
Retrocopy CTCEDMAAFITGRDG-VPADPDNIYLTTGASDGISTILKLLVSGAGKSRTGEMIPIPQYPLYSAVISELN

Parental  AVQVDYYLDEERAWALDIAELRRALCQARDR-CCPRVL-CVINPGNPTGQVQTRECIEAVIRFAFEEGLF
          AVQV.Y.LDE...WAL...ELRRAL.QA.D....P.VL.C.INPGNPT.QVQ.R.C.E.VI.FA..E.LF
Retrocopy AVQVNYILDEN-CWALNVDELRRALRQAKDH*SGPKVL>CIINPGNPTSQVQSRKCREDVICFA*KEKLF

Parental  LMADEVYQDNVYAEGSQFHSFK-KVLTE-MGPPYATQQELASFHSVSKGYMGECGFRGGYVEVVNMDAEV
          L.ADE.YQDNV......FHSFK.K..T..MG..Y....ELASFHS.SKGY.G.C..RGGY.EV.....E.
Retrocopy LLADELYQDNVCSPDCRFHSFK>KCFTR*MGHEYSSNVELASFHSTSKGYVGKCDYRGGYMEVISLHPEI

Parental  QKQMAKLMSVRLCPPVPGQALMGMVVSPPTPSEPSFKQFQAERQEVLAELAAKAKLTEQVFNEAPGIRCN
          ..Q..KL.S.RLCPPV.GQ..M..VV.PP.P.E.SF.QF..E...VL..LA.KAKLTE..FN..PGI.C.
Retrocopy EGQLVKLLSIRLCPPVSGQVAMDIVVNPPVPGEESFEQFSREKEFVLGNLAKKAKLTEDLFNQVPGIQCD

Parental  PVQGAMYSFPQIQLPLKAVQRAQDLGLAPDMFFCLCLLEETGICVVPGSGFGQQEGTYHFRMTILPPMEK
          P.Q.AMY.FP.I..P.KAV..AQ....APD......LLEETGICVVPGSGFGQ.EGTYHFRMTILPP.EK
Retrocopy PLQRAMYAFPRILIPAKAVEAAQSHKMAPDLVYYMKLLEETGICVVPGSGFGQREGTYHFRMTILPPVEK

Parental  LRVLLEKLRHFHAKFTHEYS
          L..LL.K...FH..F...YS
Retrocopy LKTLLHKV--FHLNFLEQYS

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	0.02 RPM	12.57 RPM
SRP007412_cerebellum	0.00 RPM	18.76 RPM
SRP007412_heart	0.00 RPM	35.30 RPM
SRP007412_kidney	0.04 RPM	42.33 RPM
SRP007412_liver	0.46 RPM	375.96 RPM
SRP007412_testis	0.41 RPM	2.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_382 was not detected

EST

No EST(s) were mapped for retro_mmus_382 retrocopy.

TSS

No TSS is located nearby retro_mmus_382 retrocopy 5' end.

Lab

retro_mmus_382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_382 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022546	1 retrocopy	retro_mmus_382 ,