RetrogeneDB ID: retro_mmus_2971

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:125547268..125548465(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gdi2
• Ensembl ID: ENSMUSG00000021218
• Aliases: Gdi2, GDI-B, GDIB, Gdi3
• Description: guanosine diphosphate (GDP) dissociation inhibitor 2 [Source:MGI Symbol;Acc:MGI:99845]

Sequence

>retro_mmus_2971
ATGAAAGAGGAATACAACGTGATGGTGCTGGGCACCGGCCTGACAGAATGTATCCTGTCGGGGATAATGTCAATAAATGG
AAAGAAGGTTCTTTATATGGGTCAGAATTCATACTATGGAGGAGAAAGTGCATCTATAACACCGCTGGAAGATTTATATA
AAAGATGTAAATTACCAGAACAACGGCCAGCATCAATGGGGAGAGGAAGAGACTGGAATGTTAACCTAATTCCCAAGTTC
CTTATGGCCAATGGTCAGTTGGTGAAGATGCTGCTTTTCACAGAGGTCACTCGTTATATGGACTTCAGAGTGATTGAAGG
AAGCTTTGTCTACAAGGGAGGAAAAATCTACAAGGTTCCTTCCACTGAAGCAGAAGCCCTGGCGTGTAGCTTAATGGGAC
TGTTGGAGAAACGCTGCTTCGGGAAGTTCCTGGTTTATGTTGTCAACTTTGATGAAAAAGATCCTAGAACTTTCGAAGGT
GTTGATCCTAAGAAGACCTCCATGAGAGATGTGTATAAGAAGTTTGATTTGGGCCAAGATGTTATAGACTTTACTGGCCA
TTCTCTTGCGCTGTACAGAACAGGTGGCTACTTAGATCAGCCGTGTTGTGAAACCATTAACAGAATTAAACGTTGCAGCG
AGTCTTTGGCAAGATATGGTAAAAGCCCATACCTCTATCCGCTTAATGGTCTTGGAGAATTGCTGCAAGGATTTGCAAGG
TTAAGTGCGATATATGGAGGTACCTACATGTTGAATAAACCAGTTGAAGAAATCATTGTGCAAAATGGAAAAGTGGTTAG
TGTAAAATCTGAAGGAGAGATTGCTCGCTGTAAATAGCTCATCTGTGATCCCAGCTATGTAAAAGATCGGGTTGAAAAAG
TGGGCCAGGTAGTCAGAGTGATCTGTATCCTTAGCCACCCTATCAAGAACACCAATGATGCTAAATCCTGCCAGATCGTC
ATTCCACAGAAGCAAGTCAACCGCAAGTCAGATATCTATGTCTTCATGATCTCCTTTGCACATAATGTGACAGCAAAGGG
CAAGTATATTGCCATTGTAAGTACAACCTTGGAGACCAAGGAACCAGAGAAAGAAATCAGACTGGCTTTGGAGCTCTTGG
AACCAATTGAACAGGAATTTGTCAGCATCAGTGACCTCTTTGTGCCTAAAGATTTGGGGACAGATAGATCTTCATTT

Alignment

ORF - retro_mmus_2971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 89.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNEEYDVIVLGTGLTECILSGIMSVNGKKVLHMDQNPYYGGESASITPLEDLYKRFKLPGQPPASMGRGR
          M.EEY.V.VLGTGLTECILSGIMS.NGKKVL.M.QN.YYGGESASITPLEDLYKR.KLP.Q.PASMGRGR
Retrocopy MKEEYNVMVLGTGLTECILSGIMSINGKKVLYMGQNSYYGGESASITPLEDLYKRCKLPEQRPASMGRGR

Parental  DWNVDLIPKFLMANGQLVKMLLFTEVTRYMDFKVIEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRRF
          DWNV.LIPKFLMANGQLVKMLLFTEVTRYMDF.VIEGSFVYKGGKIYKVPSTEAEALA.SLMGL.EKR.F
Retrocopy DWNVNLIPKFLMANGQLVKMLLFTEVTRYMDFRVIEGSFVYKGGKIYKVPSTEAEALACSLMGLLEKRCF

Parental  RKFLVYVANFDEKDPRTFEGVDPKKTSMRDVYKKFDLGQDVIDFTGHSLALYRTDDYLDQPCCETINRIK
          .KFLVYV.NFDEKDPRTFEGVDPKKTSMRDVYKKFDLGQDVIDFTGHSLALYRT..YLDQPCCETINRIK
Retrocopy GKFLVYVVNFDEKDPRTFEGVDPKKTSMRDVYKKFDLGQDVIDFTGHSLALYRTGGYLDQPCCETINRIK

Parental  LYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVVGVKSEGEIARCKQL
          ..SESLARYGKSPYLYPL.GLGEL.QGFARLSAIYGGTYMLNKP.EEIIVQNGKVV.VKSEGEIARCK.L
Retrocopy RCSESLARYGKSPYLYPLNGLGELLQGFARLSAIYGGTYMLNKPVEEIIVQNGKVVSVKSEGEIARCK*L

Parental  ICDPSYVKDRVEKVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISFAHNVAAQGKYI
          ICDPSYVKDRVEKVGQV.RVICILSHPIKNTNDA.SCQI.IPQ.QVNRKSDIYV.MISFAHNV.A.GKYI
Retrocopy ICDPSYVKDRVEKVGQVVRVICILSHPIKNTNDAKSCQIVIPQKQVNRKSDIYVFMISFAHNVTAKGKYI

Parental  AIVSTTVETKEPEKEIRPALELLEPIEQKFVSISDLFVPKDLGTDSQIF
          AIVSTT.ETKEPEKEIR.ALELLEPIEQ.FVSISDLFVPKDLGTD...F
Retrocopy AIVSTTLETKEPEKEIRLALELLEPIEQEFVSISDLFVPKDLGTDRSSF

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	175.81 RPM
SRP007412_cerebellum	0.04 RPM	145.16 RPM
SRP007412_heart	0.00 RPM	121.69 RPM
SRP007412_kidney	0.13 RPM	243.41 RPM
SRP007412_liver	0.03 RPM	220.22 RPM
SRP007412_testis	0.00 RPM	192.24 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2971 was not detected

EST

No EST(s) were mapped for retro_mmus_2971 retrocopy.

TSS

No TSS is located nearby retro_mmus_2971 retrocopy 5' end.

Lab

retro_mmus_2971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2971 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971 , retro_mmus_360,
Mus musculus	ENSMUSG00000025531	1 retrocopy	retro_mmus_284,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,