RetrogeneDB ID: retro_mmus_3158

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:100030557..100032099(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000071041
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Impdh2
• Ensembl ID: ENSMUSG00000062867
• Aliases: Impdh2, IMPD
• Description: inosine 5'-phosphate dehydrogenase 2 [Source:MGI Symbol;Acc:MGI:109367]

Sequence

>retro_mmus_3158
ATGGCGGACTACCTGATTAGCGGAGGCACCTCTTACGTGCCGGACGACGGGCTCACAGCGCAGCAGCTCTTCAACTGCGG
GGACGGCCTCACCTACAATGATTTTCTCATTCTTCCTGGGTATATCGACTTCACTGCAGATCAGGTGGACTTGACGTCTG
CTCTAACTAAGAAGATTACACTAAAGACCCCATTGGTTTCCTCACCCATGGACACTGTCACAGAGGCTGGAATGGCCATC
GCGATGGCGCTTACAGGAGGTATTGGTTTTATCCACCACAACTGCACACCTGAATTCCAGGCCAATGAAGTTCGGAAAGT
GAAGAAATACGAACAGGGATTCATCACTGACCCCGTGGTCCTTAGCCCCAAGGATCGTGTACGCGATGTTTTTGAGGCCA
AAGCCAGGCATGGCTTCTGTGGTATCCCCATCACAGATACAGGCCGGATGGGGAGTCGATTGGTGGGCATCATCTCCTCA
AGGGACATTGATTTCCTCAAGGAGGAAGAGCATGACCGGTTCTTGGAAGAGATCATGACTAAGAGGGAAGATTTGGTGGT
CGCCCCTGCCGGCGTCACTCTGAAAGAGGCAAATGAGATTCTGCAGCGAAGTAAAAAGGGAAAGTTGCCCATTGTGAATG
AAAATGATGAGCTGGTAGCCATCATTGCCCGGACAGACCTAAAGAAGAATCGTGATTACCCCCTGGCCTCCAAAGATGCC
AAGAAGCAACTGCTGTGTGGGGCAGCCATTGGCACTCATGAGGATGACAAGTATAGGCTGGACTTACTGGCCCTTGCTGG
TGTGGATGTAGTGGTTTTGGACTCTTCCCAGGGAAACTCCATCTTCCAAATCAATATGATCAAATACATCAAGGAGAAGT
ACCCCAGTCTGCAGGTCATTGGAGGCAATGTAGTCACTGCTGCGCAAGCCAAGAACCTCATAGATGCAGGTGTAGATGCT
TTGCGAGTCGGCATGGGAAGTGGTTCCATCTGCATCACCCAGGAAGTGTTGGCCTGTGGGCGGCCCCAAGCCACAGCAGT
GTACAAGGTCTCTGAGTATGCCCGTCGCTTTGGTGTTCCTGTTATTGCTGATGGAGGAATCCAAAATGTGGGTCATATTG
CCAAAGCTTTGGCTTTTGGGGCTTCCACAGTCATGATGGGCTCCCTCCTGGCTGCCACCACTGAGGCCCCTGGCGAGTAC
TTCTTCTCAGATGGGATCCGGCTGAAGAAATACCGAGGTATGGGTTCTCTTGATGCCATGGACAAACATCTCAGCAGCCA
GAACCGATACTTCAGTGAAGCTGACAAAATCAAAGTGGCCCAAGGAGTTTCAGGGGCAGTGCAGGACAAGGGGTCTATCC
ACAAGTTCGTTCCTTACCTGATTGCTGGCATCCAGCATTCCTGTCAGGACATTGGTGCCAAGAGTTTAACCCAAGTCAGA
GCCATGATGTACTCGGGGGAGCTTAAATTTGAGAAGAGGACATCCTCTGCTCAGGTGGAAGGTGGCGTCCACAGCCTCCA
TTCGTACGAGAAACGGCTTTTC

Alignment

ORF - retro_mmus_3158 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADYLISGGTSYVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPM
          MADYLISGGTSYVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPM
Retrocopy MADYLISGGTSYVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPM

Parental  DTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKARHGFC
          DTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKARHGFC
Retrocopy DTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKARHGFC

Parental  GIPITDTGRMGSRLVGIISSRDIDFLKEEEHDRFLEEIMTKREDLVVAPAGVTLKEANEILQRSKKGKLP
          GIPITDTGRMGSRLVGIISSRDIDFLKEEEHDRFLEEIMTKREDLVVAPAGVTLKEANEILQRSKKGKLP
Retrocopy GIPITDTGRMGSRLVGIISSRDIDFLKEEEHDRFLEEIMTKREDLVVAPAGVTLKEANEILQRSKKGKLP

Parental  IVNENDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLALAGVDVVVLDSSQGNS
          IVNENDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLALAGVDVVVLDSSQGNS
Retrocopy IVNENDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLALAGVDVVVLDSSQGNS

Parental  IFQINMIKYIKEKYPSLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKV
          IFQINMIKYIKEKYPSLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKV
Retrocopy IFQINMIKYIKEKYPSLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKV

Parental  SEYARRFGVPVIADGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAM
          SEYARRFGVPVIADGGIQNVGHIAKALA.GASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAM
Retrocopy SEYARRFGVPVIADGGIQNVGHIAKALAFGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAM

Parental  DKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKF
          DKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKF
Retrocopy DKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKF

Parental  EKRTSSAQVEGGVHSLHSYEKRLF
          EKRTSSAQVEGGVHSLHSYEKRLF
Retrocopy EKRTSSAQVEGGVHSLHSYEKRLF

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	0.21 RPM	17.24 RPM
SRP007412_cerebellum	0.09 RPM	12.16 RPM
SRP007412_heart	0.25 RPM	17.18 RPM
SRP007412_kidney	0.19 RPM	14.73 RPM
SRP007412_liver	0.08 RPM	13.71 RPM
SRP007412_testis	0.50 RPM	61.24 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3158 was not detected

EST

11 EST(s) were mapped to retro_mmus_3158 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA268386	100030507	100031084	99.9	572	1	567
AA270700	100030500	100031118	98.6	603	8	588
AA840216	100030532	100031298	98.2	735	11	711
AV451262	100030908	100031402	99.6	491	1	488
AV498953	100030908	100031420	98.7	504	7	496
AV583237	100030933	100031407	99.8	473	1	472
BE305285	100030531	100031146	99.2	599	4	589
BF162639	100030504	100031216	98.3	691	7	672
CF898718	100030686	100031396	100	635	0	634
CF898728	100030686	100031381	100	620	0	619
CK624315	100030827	100031426	100	599	0	599

TSS

No TSS is located nearby retro_mmus_3158 retrocopy 5' end.

Lab

retro_mmus_3158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3158 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009844	1 retrocopy	retro_fcat_1377,
Homo sapiens	ENSG00000178035	1 retrocopy	retro_hsap_697,
Gorilla gorilla	ENSGGOG00000013245	1 retrocopy	retro_ggor_594,
Mus musculus	ENSMUSG00000062867	1 retrocopy	retro_mmus_3158 ,
Nomascus leucogenys	ENSNLEG00000006743	7 retrocopies	retro_nleu_1126, retro_nleu_1371, retro_nleu_1378, retro_nleu_1591, retro_nleu_2183, retro_nleu_2188, retro_nleu_359,
Pongo abelii	ENSPPYG00000013884	1 retrocopy	retro_pabe_528,
Pan troglodytes	ENSPTRG00000014908	1 retrocopy	retro_ptro_501,
Rattus norvegicus	ENSRNOG00000031965	1 retrocopy	retro_rnor_1523,
Tursiops truncatus	ENSTTRG00000017349	2 retrocopies	retro_ttru_1148, retro_ttru_1665,