RetrogeneDB ID: retro_mmus_3609

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:53883613..53884420(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080968
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atf1
• Ensembl ID: ENSMUSG00000023027
• Aliases: None
• Description: activating transcription factor 1 [Source:MGI Symbol;Acc:MGI:1298366]

Sequence

>retro_mmus_3609
ATGGAAGATTCCCACAAGAGTAACACGACAGAGTCTACATCTCAGCCTGGTTCAACCGTTGCGGGGCCTCACGTTTCTCA
GATAGTACATCAGGTGTCATCATTATCAGAAAGTGAGGAGTCTCAGGACTCATCTGACAGCATAGGCTCCTCACAGAAAG
CTCACGGGATCCTGGCCCGGCGCCCATCCTACAGGAAAATTTTGAAAGACCTCTCTTCTGAAGATACACGGGGCAGAAAA
GGGGAAGGAGAAAATCCCAGCATTTCTGCCATCACGTCTATGTCTGTTCCAGCCCCCATCTATCAGACGAGCAGCGGACA
GTACATTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGCGTGCAGGCACTGCAGACATTAA
CCATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGACGGACAGCAGATACTCGTC
CCGATCAACCAGGTGGTTGTACAGACTGCATCAGGAGATATGCAGACCTACCAGATCCGTACCACACCGTCTGCCACGTT
ACTCCCACAGACAGTGGTGATGACTTCTCCTGTGACTCTTACATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAA
GAGAAATACAACTGATGAAAAACAGAGAAGCTGCCCGAGAGTGCCGCCGGAAGAAGAAGGAGTACGTGAAGTGCCTGAAG
AACCGTGTTGCTGTTCTGGAAAATCAAAATAAAACTCTAATAGAGGAGCTAAAGACTTTGAAGGACCTTTATTCTCATAA
AAGTGTT

Alignment

ORF - retro_mmus_3609 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDSHKSNTTETASQPGSTVAGPHVSQIVHQVSSLSESEESQDSSDSIGSSQKAHGILARRPSYRKILKD
          MEDSHKSNTTE..SQPGSTVAGPHVSQIVHQVSSLSESEESQDSSDSIGSSQKAHGILARRPSYRKILKD
Retrocopy MEDSHKSNTTESTSQPGSTVAGPHVSQIVHQVSSLSESEESQDSSDSIGSSQKAHGILARRPSYRKILKD

Parental  LSSEDTRGRKGEGENPSISAITSMSVPAPIYQTSSGQYIAIAPNGALQLASPSTDGVQALQTLTMTNSSS
          LSSEDTRGRKGEGENPSISAITSMSVPAPIYQTSSGQYIAIAPNGALQLASPSTDGVQALQTLTMTNSSS
Retrocopy LSSEDTRGRKGEGENPSISAITSMSVPAPIYQTSSGQYIAIAPNGALQLASPSTDGVQALQTLTMTNSSS

Parental  TQQGTILQYAQTSDGQQILVPSNQVVVQTASGDMQTYQIRTTPSATSLPQTVVMTSPVTLASQTTKTDDP
          TQQGTILQYAQTSDGQQILVP.NQVVVQTASGDMQTYQIRTTPSAT.LPQTVVMTSPVTL.SQTTKTDDP
Retrocopy TQQGTILQYAQTSDGQQILVPINQVVVQTASGDMQTYQIRTTPSATLLPQTVVMTSPVTLTSQTTKTDDP

Parental  QLRREIRLMKNREAARECRRKKKEYVKCLENRVAVLENQNKTLIEELKTLKDLYSHKSV
          QLRREI.LMKNREAARECRRKKKEYVKCL.NRVAVLENQNKTLIEELKTLKDLYSHKSV
Retrocopy QLRREIQLMKNREAARECRRKKKEYVKCLKNRVAVLENQNKTLIEELKTLKDLYSHKSV

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	0.02 RPM	7.50 RPM
SRP007412_cerebellum	0.04 RPM	9.73 RPM
SRP007412_heart	0.03 RPM	27.55 RPM
SRP007412_kidney	0.08 RPM	22.68 RPM
SRP007412_liver	0.08 RPM	19.33 RPM
SRP007412_testis	0.37 RPM	54.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3609 was not detected

EST

No EST(s) were mapped for retro_mmus_3609 retrocopy.

TSS

No TSS is located nearby retro_mmus_3609 retrocopy 5' end.

Lab

retro_mmus_3609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3609 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004733	5 retrocopies	retro_chof_1987, retro_chof_2305, retro_chof_27, retro_chof_462, retro_chof_760,
Erinaceus europaeus	ENSEEUG00000008000	2 retrocopies	retro_eeur_332, retro_eeur_704,
Homo sapiens	ENSG00000123268	1 retrocopy	retro_hsap_3633,
Mus musculus	ENSMUSG00000023027	1 retrocopy	retro_mmus_3609 ,
Oryctolagus cuniculus	ENSOCUG00000017023	1 retrocopy	retro_ocun_383,
Procavia capensis	ENSPCAG00000010038	2 retrocopies	retro_pcap_303, retro_pcap_442,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635,