RetrogeneDB ID: retro_mmus_1253

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:19350750..19351647(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ggps1
• Ensembl ID: ENSMUSG00000021302
• Aliases: Ggps1, 1810026C22Rik, 9530089B04Rik, AI843169, C79210
• Description: geranylgeranyl diphosphate synthase 1 [Source:MGI Symbol;Acc:MGI:1341724]

Sequence

>retro_mmus_1253
ATGGAGAAAACTAAAGAGAAAGCTGAAAGAATTCTTCTAGACCCTTATAGGTACTTACTTCAGTTACCAGGTAAACAGGT
GAGAACCAAACTTTCGCAGGCATTTAATCACTGGCTGAAAGTTCCAGAAGACAAGCTACAGATTATCATTGAAGTGACTG
AAATGTTGCATAATGCCAGTTTACTCATTGATGATATTGAAGACAGTTCAAAGCTCCGACATGGTTTCCCAGTGGCTCAC
AGCATCTGTGGTGTCCCATCTGTCATTAATTCTGCCAATTATGTCTACTTCCTTGGACTGGAAAAAGTCTTAACCCTTGA
TCACCCAGATGCGATGAAGCTTTTCACACGCCAGCTTCTGGAACTTCATCAGGGACAAGGCCTCGATATTTACTGGAGGG
ACACCTACACTTGTCCAACTGAAGAAGAATATAAAGCCATGGTGTTGCAGAAGACAGGTGGTTCGTTTGGATTAGTAGTA
GGTCTTATGCAGTTCTCTGATTTCAAAGAAGATCTAAAGCCACTGCTTGATACACTTGGGCTCTTTTTCCAGATTAGAGA
TGATTATGCCAATCTACACTCCAAAGAATACAGTGAAAACAAAAGTTTCTGTGAAGACTTGACAGAAGGGAAGTTCTAAT
TCCCCACTATCCATGCCATTTGGTCAAGGCCAGAAAGCACCCAGGTACAGAACATCCTGCACCAGAGAACAGAGACTATA
GATATTAAAAAGTATTGTGTGCAGTACCTGAAGGATGTAGGTACTTTTGCATACACTCGACACACTCTTAGAGAGCTTGA
AGCTAAAGCCTGCAAACAAATTGAGGCCTGTGGTGGGAACCCTTCACTAGTGGCTTTAGTCAAGCACTTAAGTAAGATGT
TCACAGAAGAAAATGAA

Alignment

ORF - retro_mmus_1253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKTKEKAERILLEPYRYLLQLPGKQVRSKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDSS
          MEKTKEKAERILL.PYRYLLQLPGKQVR.KLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDSS
Retrocopy MEKTKEKAERILLDPYRYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDSS

Parental  KLRRGFPVAHSIYGVPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLELHQGQGLDIYWRDTYTCPT
          KLR.GFPVAHSI.GVPSVINSANYVYFLGLEKVLTLDHPDA.KLFTRQLLELHQGQGLDIYWRDTYTCPT
Retrocopy KLRHGFPVAHSICGVPSVINSANYVYFLGLEKVLTLDHPDAMKLFTRQLLELHQGQGLDIYWRDTYTCPT

Parental  EEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLLDTLGLFFQIRDDYANLHSKEYSENKSFCEDLTE
          EEEYKAMVLQKTGG.FGL.VGLMQ.FSD.KEDLKPLLDTLGLFFQIRDDYANLHSKEYSENKSFCEDLTE
Retrocopy EEEYKAMVLQKTGGSFGLVVGLMQ-FSDFKEDLKPLLDTLGLFFQIRDDYANLHSKEYSENKSFCEDLTE

Parental  GKFSFPTIHAIWSRPESTQVQNILRQRTENIDIKKYCVQYLEDVGSFAYTRHTLRELEAKAYKQIEACGG
          GKF.FPTIHAIWSRPESTQVQNIL.QRTE.IDIKKYCVQYL.DVG.FAYTRHTLRELEAKA.KQIEACGG
Retrocopy GKF*FPTIHAIWSRPESTQVQNILHQRTETIDIKKYCVQYLKDVGTFAYTRHTLRELEAKACKQIEACGG

Parental  NPSLVALVKHLSKMFTEENK
          NPSLVALVKHLSKMFTEEN.
Retrocopy NPSLVALVKHLSKMFTEENE

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	24.79 RPM
SRP007412_cerebellum	0.00 RPM	17.98 RPM
SRP007412_heart	0.00 RPM	8.78 RPM
SRP007412_kidney	0.04 RPM	10.09 RPM
SRP007412_liver	0.03 RPM	3.39 RPM
SRP007412_testis	0.00 RPM	5.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1253 was not detected

EST

No EST(s) were mapped for retro_mmus_1253 retrocopy.

TSS

No TSS is located nearby retro_mmus_1253 retrocopy 5' end.

Lab

retro_mmus_1253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1253 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011303	1 retrocopy	retro_cfam_1438,
Echinops telfairi	ENSETEG00000008916	1 retrocopy	retro_etel_1265,
Myotis lucifugus	ENSMLUG00000016813	1 retrocopy	retro_mluc_54,
Mus musculus	ENSMUSG00000021302	1 retrocopy	retro_mmus_1253 ,
Ictidomys tridecemlineatus	ENSSTOG00000004263	1 retrocopy	retro_itri_619,