RetrogeneDB ID: retro_mmus_844

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:7859899..7860904(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000073233
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nfyc
• Ensembl ID: ENSMUSG00000032897
• Aliases: None
• Description: nuclear transcription factor-Y gamma [Source:MGI Symbol;Acc:MGI:107901]

Sequence

>retro_mmus_844
ATGTCCACAGAAGGAGGGTTTGGCGGTACCAGCAGCAGTGATGCCCAGCAAAGCCTCCAGTCCTTCTGGCCCAGAGTCAT
GGAAGAAATCCGAAACTTAACAGTGAAAGATTTCCGAGTACAGGAACTCCCACTGGCTCTTATTAAGAAGATTATGAAAC
TGGATGAAGATGTGAAGATGATCAGTGCAGAAGCCCCTGTGCTGTTTGCTAAGGCAGCCCAGATTTTTATCACTGAGCTG
ACTCTTCGAGCCTGGATCCACACAGAGGATAACAAGCGTCGTACTCTTCAGAGGAATGATATTGCCATGGCAATTACAAA
ATTTGATCAGTTCGACTTTCTCATCGATATTGTTCCAAGAGATGAACTGAAACCTCCAAAGCGCCAGGAGGAGGTACGCC
AGTCTGTGACTCCTGCGAAGCCTGTCCAGTACTACTTCACGCTGGCTCAGCAGCCCACTGCTGTCCAGGTCCAGGGACAG
CAGCAAGGCCAGCAGACCACCAGTTCTACGACCACCATCCAGCCTGGACAGATCATCATTGCACAGCCTCAGCAGGGTCA
GATCACACCCGTGACCATGCAGGTTGGAGAAGGTCAGCAGGTGCAGATTGTACAGGCCCAACCTCAGGGTCAGGCCCAGC
AGACCCAGAGTGGCACTGGACAGACCATGCAGGTGATGCAGCAGATCATTACCAACACAGGAGAGATCCAACAGATCCCG
GTGCAGCTGAATGCTGGCCAGCTGCAATATATCCGATTAGCCCAGCCTGTATCAGGCACCCAAGTTGTCCAAGGACAGAT
CCAGACACTTGCTACCAACGCCCAACAGATCACACAGACAGAGGTCCAGCAAGGAAAGCAGCAGTTCAGCCAGTTCACAG
ATGGACAGCAGCTGTACCAGATCCAGCAAGTCACCATGCCTGCAGGCCAAGACCTCGCCCAGCCCATGTTTATTCAGTCA
GCCAATCAGCCCTCTGATGGGCAGACCCCCCAGGTGACTGGAGAC

Alignment

ORF - retro_mmus_844 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFA
          MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLA.IKKIMKLDEDVKMISAEAPVLFA
Retrocopy MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLALIKKIMKLDEDVKMISAEAPVLFA

Parental  KAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAE
          KAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPA.
Retrocopy KAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAK

Parental  PVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQPQG
          PVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQ.TPVTMQVGEGQQVQIVQAQPQG
Retrocopy PVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQITPVTMQVGEGQQVQIVQAQPQG

Parental  QAQQTQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQITQT
          QAQQTQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQITQT
Retrocopy QAQQTQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQITQT

Parental  EVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQTPQVTGD
          EVQQG.QQFSQFTDGQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQTPQVTGD
Retrocopy EVQQGKQQFSQFTDGQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQTPQVTGD

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	0.07 RPM	17.22 RPM
SRP007412_cerebellum	0.00 RPM	27.53 RPM
SRP007412_heart	0.06 RPM	21.23 RPM
SRP007412_kidney	0.17 RPM	27.93 RPM
SRP007412_liver	0.03 RPM	7.95 RPM
SRP007412_testis	0.05 RPM	7.27 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_844 was not detected

EST

No EST(s) were mapped for retro_mmus_844 retrocopy.

TSS

No TSS is located nearby retro_mmus_844 retrocopy 5' end.

Lab

retro_mmus_844 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_844 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33,
Bos taurus	ENSBTAG00000021943	1 retrocopy	retro_btau_1338,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Homo sapiens	ENSG00000066136	2 retrocopies	retro_hsap_4280, retro_hsap_4668,
Gorilla gorilla	ENSGGOG00000007360	2 retrocopies	retro_ggor_2865, retro_ggor_2896,
Macropus eugenii	ENSMEUG00000004480	1 retrocopy	retro_meug_1145,
Macaca mulatta	ENSMMUG00000014970	2 retrocopies	retro_mmul_1202, retro_mmul_2485,
Mus musculus	ENSMUSG00000032897	1 retrocopy	retro_mmus_844 ,
Otolemur garnettii	ENSOGAG00000012614	2 retrocopies	retro_ogar_2147, retro_ogar_411,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102,