RetrogeneDB ID: retro_mmus_2889

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:4909037..4909825(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Phgdh
• Ensembl ID: ENSMUSG00000053398
• Aliases: Phgdh, 3-PGDH, 3PGDH, 4930479N23, A10, PGAD, PGD, PGDH, SERA
• Description: 3-phosphoglycerate dehydrogenase [Source:MGI Symbol;Acc:MGI:1355330]

Sequence

>retro_mmus_2889
ATGGCCTTTGCAAATCTGAGCAAAGTACTCATCAGTGACAGCCTGGAGCCCTGCTGCCGGAAGATCCTGCAAGATGGAGG
GCTGCAGGTGGTGGAGAAGCAGAACTTGAGCAAGAAGGAGCTGACAGCCGAGCTGCAGGACTGTGAAGGCATTATTGTCC
GGTCAGCTACTAAGGTCACTGCTGTTGTCATCAATGCAGCAGAGAAGCTCCAGGCGGTGGGCAGGGCTAGTACAGGCGTG
GACAATGTGGCTCTGGAGGCTGCCATGAGGAAGGACATCTTAGTCATGAACACCCCCAATGCAAACAGCATCAGTGCTGC
GGAGTTCACCTGTGGGATGATCATGTGTCTGGCCAGGCAGATTCTCCAGGCGACGGCTTCGATGAAAGATGGCAAATGGG
ACCGGAAGAAGTTCACGGGACAGAATTGAACGGGAAGATACTGGGAATTCTTGGCCTAGGCAGAATCGGAAGAGAGGTGG
CCACCTGAATGCAGTCCTTTGGAATGAAGACTGTAGGCTATGACCCCGTCATCTCTCCTGAAGTCGCGGCCTCCTTTGGT
GTTCAGCAGCTGCCGCTGGAGGAGATCTGGCCTCTCTGTGATTTCATAACTATCTATACCCCTCTCCTGCCCTCCACCAC
AGGCTTGCTGCATGACAGCACCTTTGCTCAGTGCAAGAAAGGCGTGCGAGTGGTGAACTGTGCTCGAGGAGGCATTGTGG
ATGAAGGTGGCCTGCGGTCTGGTCAATGTGCTGGGGCTGCACTGGATATATTTACAGAAGAGCCACCA

Alignment

ORF - retro_mmus_2889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 50.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAFANLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKL
          MAFANL.KVLISDSL.PCCRKILQDGGLQVVEKQNLSK.EL.AELQDCEG.IVRSATKVTA.VINAAEKL
Retrocopy MAFANLSKVLISDSLEPCCRKILQDGGLQVVEKQNLSKKELTAELQDCEGIIVRSATKVTAVVINAAEKL

Parental  QVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWDRKKFM-
          Q.VGRA.TGVDNV.LEAA.RK.ILVMNTPN.NS.SAAE.TCGMIMCLARQI.QATASMKDGKWDRKKF..
Retrocopy QAVGRASTGVDNVALEAAMRKDILVMNTPNANSISAAEFTCGMIMCLARQILQATASMKDGKWDRKKFT<

Parental  GTELNGKTLGILGLGRIGREVATRMQSFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPL
          GTELNGK.LGILGLGRIGREVAT.MQSFGMKTVGYDP.ISPEVAASFGVQQLPLEEIWPLCDFIT..TPL
Retrocopy GTELNGKILGILGLGRIGREVAT*MQSFGMKTVGYDPVISPEVAASFGVQQLPLEEIWPLCDFITIYTPL

Parental  LPSTTGLLNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPP
          LPSTTGLL.DSTFAQCKKGVRVVNCARGGIVDEG.L.....SGQCAGAALD.FTEEPP
Retrocopy LPSTTGLLHDSTFAQCKKGVRVVNCARGGIVDEGGL----RSGQCAGAALDIFTEEPP

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	0.16 RPM	21.05 RPM
SRP007412_cerebellum	0.00 RPM	11.94 RPM
SRP007412_heart	0.03 RPM	0.59 RPM
SRP007412_kidney	0.04 RPM	5.64 RPM
SRP007412_liver	0.00 RPM	0.08 RPM
SRP007412_testis	0.18 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2889 was not detected

EST

No EST(s) were mapped for retro_mmus_2889 retrocopy.

TSS

No TSS is located nearby retro_mmus_2889 retrocopy 5' end.

Lab

retro_mmus_2889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2889 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019916	4 retrocopies	retro_cjac_2894, retro_cjac_2958, retro_cjac_3441, retro_cjac_3994,
Myotis lucifugus	ENSMLUG00000002986	1 retrocopy	retro_mluc_2502,
Mus musculus	ENSMUSG00000053398	16 retrocopies	retro_mmus_1008, retro_mmus_1223, retro_mmus_1384, retro_mmus_1708, retro_mmus_1835, retro_mmus_1892, retro_mmus_2057, retro_mmus_2169, retro_mmus_2889 , retro_mmus_2979, retro_mmus_3021, retro_mmus_3176, retro_mmus_3180, retro_mmus_3217, retro_mmus_3441, retro_mmus_545,
Rattus norvegicus	ENSRNOG00000019328	1 retrocopy	retro_rnor_452,