RetrogeneDB ID: retro_mmus_1476

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:65793551..65794338(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gps2
• Ensembl ID: ENSMUSG00000023170
• Aliases: Gps2, AI505953
• Description: G protein pathway suppressor 2 [Source:MGI Symbol;Acc:MGI:1891751]

Sequence

>retro_mmus_1476
TCCCAGGAACAAATTCTGAAGCTGCAGGAGAAGCTTTCAGCTCTACAGGAGGAGAAACACCAGCTTTTCTTGCAGCTCAA
GAAAGTTTTGCATGAAGAAGAAAAACGGAGGTGAAAAGAACAGAGTGACTTAACCGCTCTGAAGTCAGCTGCATACCAGC
AGAGCCTGAAGATTCATACAGGAACTCACTTCCTCAGCATGCAGGGGTATCCTGGAGGACACAATCGCCCAGGTACTCTC
ATGGCAGCTGACAGAGCCAAGCAGATGTTTGGACCACAAGTGCTTACGACCCGGCACTACGTGGGATCAGCAGCTGCTTC
TGCAGGAACCCCAGAACATGGACAATTCCAAGGCAGTCCAGGGGGTGCTTTTGGGACTGCTGAGCCCCCACCTCATTATG
GGCCAATACAACCAGCCTATAGTCCTAGCCAGCAGCTCAGAGCCCTTCAGCATTTCCTGCAGTGCAGTACCTGTCTCAGC
CACAGCCACAACCCTATGCAGTGCATGGCCACTTTCAGCCCACTCAGACAGGGTTCTTCCAACCGGCAGTGCCCTCTCTT
TGCAAAAACAGATGGAGCATGCCAACCAGGAGACCAGCTTCACTGAGTCATCTTCTTTGTGGCCCATGCACTCGCAAGTT
CTGCATCTAGCCCCTGGACTCCTGGCTTACCCCCAGCTCCCCATAGAGATACAAGCAGCAGGGAAATCAGGGTTTGCCAC
CACCAGCCATCCTGGCCCCCGACTCCCTGTCATACAACACAACCAGAACCCACGATTCTATGACAAG

Alignment

ORF - retro_mmus_1476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.3 %
• Parental protein coverage: 80.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TKEQILKLQEKLSALQEEKHQLFLQLKKVLHEEEKRRRKEQSDLTTLTSAAYQQSLTVHTGTHLLSMQGS
          ..EQILKLQEKLSALQEEKHQLFLQLKKVLHEEEKRR.KEQSDLT.L.SAAYQQSL..HTGTH.LSMQG.
Retrocopy SQEQILKLQEKLSALQEEKHQLFLQLKKVLHEEEKRR*KEQSDLTALKSAAYQQSLKIHTGTHFLSMQGY

Parental  PGGHNRPGTLMAADRAKQMFGPQVLTTRHYVGSAAAFAGTPEHGQFQGSPGGAYGTAQPPPHYGPTQPAY
          PGGHNRPGTLMAADRAKQMFGPQVLTTRHYVGSAAA.AGTPEHGQFQGSPGGA.GTA.PPPHYGP.QPAY
Retrocopy PGGHNRPGTLMAADRAKQMFGPQVLTTRHYVGSAAASAGTPEHGQFQGSPGGAFGTAEPPPHYGPIQPAY

Parental  SPSQQLRA-PSAFPAVQYLSQPQPQPYAVHGHFQPTQTGFLQP-GSTLSLQKQMEHANQQTSFSDSSSLR
          SPSQQLRA.PSAFPAVQYLSQPQPQPYAVHGHFQPTQTGF.QP.GS.LSLQKQMEHANQ.TSF..SSSL.
Retrocopy SPSQQLRA<PSAFPAVQYLSQPQPQPYAVHGHFQPTQTGFFQP<GSALSLQKQMEHANQETSFTESSSLW

Parental  PMHPQALHPAPGLLASPQLPVQIQAAGKSGFATTSQPGPRLPFIQHSQNPRFYHK
          PMH.Q.LH.APGLLA.PQLP..IQAAGKSGFATTS.PGPRLP.IQH.QNPRFY.K
Retrocopy PMHSQVLHLAPGLLAYPQLPIEIQAAGKSGFATTSHPGPRLPVIQHNQNPRFYDK

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	17.27 RPM
SRP007412_cerebellum	0.00 RPM	36.56 RPM
SRP007412_heart	0.00 RPM	25.25 RPM
SRP007412_kidney	0.06 RPM	32.07 RPM
SRP007412_liver	0.00 RPM	17.37 RPM
SRP007412_testis	0.14 RPM	142.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1476 was not detected

EST

No EST(s) were mapped for retro_mmus_1476 retrocopy.

TSS

No TSS is located nearby retro_mmus_1476 retrocopy 5' end.

Lab

retro_mmus_1476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1476 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016576	2 retrocopies	retro_amel_1236, retro_amel_362,
Equus caballus	ENSECAG00000010635	2 retrocopies	retro_ecab_124, retro_ecab_480,
Homo sapiens	ENSG00000132522	2 retrocopies	retro_hsap_2738, retro_hsap_4222,
Gorilla gorilla	ENSGGOG00000001672	1 retrocopy	retro_ggor_1907,
Macropus eugenii	ENSMEUG00000010645	2 retrocopies	retro_meug_1327, retro_meug_182,
Myotis lucifugus	ENSMLUG00000026169	1 retrocopy	retro_mluc_1045,
Mus musculus	ENSMUSG00000023170	1 retrocopy	retro_mmus_1476 ,
Nomascus leucogenys	ENSNLEG00000009364	2 retrocopies	retro_nleu_2477, retro_nleu_600,
Pan troglodytes	ENSPTRG00000023046	1 retrocopy	retro_ptro_1852,
Pteropus vampyrus	ENSPVAG00000005052	1 retrocopy	retro_pvam_35,
Sus scrofa	ENSSSCG00000017940	1 retrocopy	retro_sscr_742,