RetrogeneDB ID: retro_mmus_2225

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:13838874..13840228(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gdap2
• Ensembl ID: ENSMUSG00000027865
• Aliases: Gdap2, C77050, D3Ertd801e
• Description: ganglioside-induced differentiation-associated-protein 2 [Source:MGI Symbol;Acc:MGI:1338001]

Sequence

>retro_mmus_2225
AGATCACCTTTTCTTTATCATTGGGACATTGATGTAAAAGTGGTTCTTTGGAAAGAAGACGTGGCATCACTGAACTGTAC
AGCCATTGTGAATACTAGCAATGAAAACTTCACAGATAAGAATCCTGTGTCAGAGAGCACCTTCATGCTTGGGGGTCGTA
TCTGAAAGAAGAACTACAGAAATTTAAAGGTTGCTGAACTGGTGAAGCAAAATTGACAAAAGGCTTTAACCTAGCTGCTC
CGTTCATCATTCACATGGTGGGACCTAAGTACAAGAGCCGCTATCGCACTGCAGCGGAGAGTTCCCTGTACAGCTGTTAC
AGAAATGTGCTTCAGCTGGCAAAAGAACAGTCCGTGTCTTCTGTTGGCTTCTGTGTCATCAATTCTGCAAAGCAAGGTTA
TCCGCTAGAGGATGCAACACACATCGCTCTTCATACTGTGAAGCAGTTCCTAGAGATCCATGGGGAAACGAATTGAAAAA
GTAGTATTTGCTGTCTCAGAACTCGAAGAGGCCACTTACCAAAAGCTGCTAACTCTGTACTTCCCAAGGTCGTTAAAGGA
GGAGAGCTGGTCATTGTTGTACCTACCTGCAGACTTTGGAAATGCAGAGGGGGAGCCCGTGGTGCCTGAGCAGCAAATGG
GTAAGCAAGAAACCTGGTGCTTCAGAGGGCAGTGAAGAAGATGAGGATGAAGGCTTGGGAATGGATCTGTCTTACTTTGG
CTCTCATGCTTTTGCTCGAATGGAAGGAGGTATTGGCAAGCAAAGAAAATTGATTATCCAGGGACAGTTGTCCAAAGATG
TCCTGCAGACACAGCATCAAAGAATTTATAATCACTGATTCTACCAATCAAGATCTGAAGACCTGTCTGATATTGCTTCT
CTGAAAGCTTTATACCAAGCAGGTGTAGATAACTGTGGCCACACAGTGATGGTGGTCATTGGAAGAAACATTCCTGTGAC
ATTGATAGATATGGACAAGGCACTCTTGTATTTTATCCGTGTAATGGATCACATCACTGTGAAGGAATATGCCTTGGTGT
ATTTTGACACACTTAGCGGCGAAGACAATCACCTGGACTGCAACTTCCTGAAGAAACTCTATGATGTCGACATCAAATGC
AAGAGGAATTTGAAGGCTCTTTATTTCATTCATCCAACATTCCACTCAAAGGTCTCAACATGGTTTATCCCTACCTTTTC
TGTCTCAGGATTGAAGGACAAGATCCACCACGTAGGGAGCCTGCAACAGCTCTTCTCTGCCATATCACCAGAGCAGATAG
ACTTTCCTCATTTTGTCCTTGAATGTGATGCCAGGGAAAATGGGCCTTATTTTGCATCTTATCCTTCATCACCT

Alignment

ORF - retro_mmus_2225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.53 %
• Parental protein coverage: 91.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RSPFVYSRDVNGKVVLWKGDVALLNCTAIVNTSNESLTDKNPVSESIFMLAG-PDLKEDLQKLKGCRTGE
          RSPF.Y..D...KVVLWK.DVA.LNCTAIVNTSNE..TDKNPVSES.FML.G...LKE.LQK.KGC.TGE
Retrocopy RSPFLYHWDIDVKVVLWKEDVASLNCTAIVNTSNENFTDKNPVSESTFMLGG<SYLKEELQKFKGC*TGE

Parental  AKLTKGFNLAARFIIHTVGPKYKSRYRTAAESSLYSCYRNVLQLAKEQSMSSVGFCVINSAKRGYPLEDA
          AKLTKGFNLAA.FIIH.VGPKYKSRYRTAAESSLYSCYRNVLQLAKEQS.SSVGFCVINSAK.GYPLEDA
Retrocopy AKLTKGFNLAAPFIIHMVGPKYKSRYRTAAESSLYSCYRNVLQLAKEQSVSSVGFCVINSAKQGYPLEDA

Parental  THIALRTVRRFLEIHGE-NIEKVVFAVSELEEATYQKLLPLYFPRSLKEEIRSLPYLPADIGNAEGEPVV
          THIAL.TV..FLEIHGE..IEKVVFAVSELEEATYQKLL.LYFPRSLKEE..SL.YLPAD.GNAEGEPVV
Retrocopy THIALHTVKQFLEIHGE>RIEKVVFAVSELEEATYQKLLTLYFPRSLKEESWSLLYLPADFGNAEGEPVV

Parental  PERQIRISE-KPGASEDNEEEDEDEGLGVDLSFIGSHAFARMEGDIDKQRKLILQGQLSEAALQKQHQRN
          PE.Q....E.........E.ED..EGLG.DLS..GSHAFARMEG.I.KQRKLI.QGQLS...LQ.QHQR.
Retrocopy PEQQMGKQE>PGASEGSEEDED--EGLGMDLSYFGSHAFARMEGGIGKQRKLIIQGQLSKDVLQTQHQRI

Parental  YNRWLCQARSEDLSDIASLKALYQTGVDNCGRTVMVVVGRNIPVTLIDMDKALLYFIHVMDHIAVKEYVL
          YN....Q.RSEDLSDIASLKALYQ.GVDNCG.TVMVV.GRNIPVTLIDMDKALLYFI.VMDHI.VKEY.L
Retrocopy YNH*FYQSRSEDLSDIASLKALYQAGVDNCGHTVMVVIGRNIPVTLIDMDKALLYFIRVMDHITVKEYAL

Parental  VYFHTLTSDYNHLDSDFLKKLYDVVDIKYKRNLKAVYFVHPTFRSKVSTWFFTTFSVSGLKDKIHHVDSL
          VYF.TL....NHLD..FLKKLYD.VDIK.KRNLKA.YF.HPTF.SKVSTWF..TFSVSGLKDKIHHV.SL
Retrocopy VYFDTLSGEDNHLDCNFLKKLYD-VDIKCKRNLKALYFIHPTFHSKVSTWFIPTFSVSGLKDKIHHVGSL

Parental  QQLFSAISPEQIDFPPFVLEYDARENGPYFASYPPSP
          QQLFSAISPEQIDFP.FVLE.DARENGPYFASYP.SP
Retrocopy QQLFSAISPEQIDFPHFVLECDARENGPYFASYPSSP

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	0.09 RPM	28.78 RPM
SRP007412_cerebellum	0.56 RPM	25.05 RPM
SRP007412_heart	0.00 RPM	7.22 RPM
SRP007412_kidney	0.00 RPM	12.76 RPM
SRP007412_liver	0.00 RPM	21.08 RPM
SRP007412_testis	0.00 RPM	21.41 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2225 was not detected

EST

No EST(s) were mapped for retro_mmus_2225 retrocopy.

TSS

No TSS is located nearby retro_mmus_2225 retrocopy 5' end.

Lab

retro_mmus_2225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2225 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012907	2 retrocopies	retro_chof_1607, retro_chof_2559,
Echinops telfairi	ENSETEG00000004391	1 retrocopy	retro_etel_530,
Felis catus	ENSFCAG00000003468	1 retrocopy	retro_fcat_1125,
Mus musculus	ENSMUSG00000027865	1 retrocopy	retro_mmus_2225 ,
Mus musculus	ENSMUSG00000068205	1 retrocopy	retro_mmus_1381,