RetrogeneDB ID: retro_mmus_1583

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:58593616..58594840(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000046952
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Glcci1
• Ensembl ID: ENSMUSG00000029638
• Aliases: Glcci1, 2310047L21Rik, A130036A18Rik, Fam117c, Gig18, Tssn1
• Description: glucocorticoid induced transcript 1 [Source:MGI Symbol;Acc:MGI:2179717]

Sequence

>retro_mmus_1583
AGCTCACCTGAGAGACGGAGTCCCGGCTCGCCCGTGTGCAGAGTGGACAGGCCAAAATCTCAACATATTCGAACCTCTAG
TACAATAAGGCGAACCTCTTCTCTGGATACGATAACAGGACCTTACCTCACAGGACAGTGGCCACGGGACCCTCATGTTC
ACTACCCTTCATGCATGAGAGATAAAGCCACTCAGACACCTAGTTGCTGGGCAGAAGAGGGAGCAGAAAAACGATCACAT
CAGCGCTCTGTATCATGGGGAAGTGCTGATCAACTGAAAGAGATTGCCAAACTAAGGCAACAGCTACAACGCAGCAAGCA
AAGTAGTCGGCATAGTAAAGAGAAGGACAGACAGTCACCTCTCCATGGCAACCACATAACAATCAGTCATACTCAGGCTA
TTGGATCAAGATCAGTCCCTATGCCTCTGTCAAACATATCAGTGCCAAAATCATCTGTTTCCCGTGTACCCTGCAATGTA
GAAGGAATAAGTCCTGAATTGGAAAAGGTGTTCATCAAAGAAAACAATGGAAAGGAAGAAGTGTCCAAGCCGTTGGATAT
ACCAGATGGTCGAAGAGCTCCACTGCCTGCTCACTACAGGAGCAGTAGTACTCGAAGCATAGATACCCAGACACCTTCTG
TCCAAGAGCGCAGCAGTAGCTGCAGCAGCCACTCCCCTTGTGTGTCCCCATTTTGTCCTCGGGAATCCCAGGATGGAAGT
CCTTGTTCAACAGAAGATTTGCTCTATGATCGTGATAAAGACAGTGGGAGTAGCTCACCGTTTCCCAAGTATGCTTCATC
TCCCAAACCCAACAACAGCTACATGTTCAAACAGGAGCCCCCAGAGGGATGTGAGCGAGTAAAGGTCTTTGAGGAAATGG
CGTCTCGTCAGCCTATCTCGGCCCCTCTCTTTTCATGTCCTGACAAAAACAAGGTTAATTTCATCCCAACCGGATCAGCT
TTCTGTCCTGTAAAACTTCTAGGCCCTCTCTTACCTGCCTCTGACCTGATGCTCAAGAACTCTCCTAATTCTGGCCAGAG
CTCGGCTCTGGCAACACTGACCGTAGAGCAGCTTTCCTCCCGGGTTTCCTTCACATCTCTCTCTGATGACACCAGCACAG
CCGACTCCCTGGAGCCCTCTGCCCAGCAGCCATCTCAGCAGCAGCAGCTCCTACAGGACTTGCAGGTGGAGGAACAGGTC
TCCACTCAGAACTATGTGATGATC

Alignment

ORF - retro_mmus_1583 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.77 %
• Parental protein coverage: 75.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSPERRSPGSPVCRVDRPKSQHIRTSSTIRRTSSLDTITGPYLTGQWPRDPHVHYPSCMRDKATQTPSCW
          SSPERRSPGSPVCRVDRPKSQHIRTSSTIRRTSSLDTITGPYLTGQWPRDPHVHYPSCMRDKATQTPSCW
Retrocopy SSPERRSPGSPVCRVDRPKSQHIRTSSTIRRTSSLDTITGPYLTGQWPRDPHVHYPSCMRDKATQTPSCW

Parental  AEEGAEKRSHQRSASWGSADQLKEIAKLRQQLQRSKQSSRHSKEKDRQSPLHGNHITISHTQAIGSRSVP
          AEEGAEKRSHQRS.SWGSADQLKEIAKLRQQLQRSKQSSRHSKEKDRQSPLHGNHITISHTQAIGSRSVP
Retrocopy AEEGAEKRSHQRSVSWGSADQLKEIAKLRQQLQRSKQSSRHSKEKDRQSPLHGNHITISHTQAIGSRSVP

Parental  MPLSNISVPKSSVSRVPCNVEGISPELEKVFIKENNGKEEVSKPLDIPDGRRAPLPAHYRSSSTRSIDTQ
          MPLSNISVPKSSVSRVPCNVEGISPELEKVFIKENNGKEEVSKPLDIPDGRRAPLPAHYRSSSTRSIDTQ
Retrocopy MPLSNISVPKSSVSRVPCNVEGISPELEKVFIKENNGKEEVSKPLDIPDGRRAPLPAHYRSSSTRSIDTQ

Parental  TPSVQERSSSCSSHSPCVSPFCPPESQDGSPCSTEDLLYDRDKDSGSSSPLPKYASSPKPNNSYMFKREP
          TPSVQERSSSCSSHSPCVSPFCP.ESQDGSPCSTEDLLYDRDKDSGSSSP.PKYASSPKPNNSYMFK.EP
Retrocopy TPSVQERSSSCSSHSPCVSPFCPRESQDGSPCSTEDLLYDRDKDSGSSSPFPKYASSPKPNNSYMFKQEP

Parental  PEGCERVKVFEEMASRQPISAPLFSCPDKNKVNFIPTGSAFCPVKLLGPLLPASDLMLKNSPNSGQSSAL
          PEGCERVKVFEEMASRQPISAPLFSCPDKNKVNFIPTGSAFCPVKLLGPLLPASDLMLKNSPNSGQSSAL
Retrocopy PEGCERVKVFEEMASRQPISAPLFSCPDKNKVNFIPTGSAFCPVKLLGPLLPASDLMLKNSPNSGQSSAL

Parental  ATLTVEQLSSRVSFTSLSDDTSTADSLEPSAQQPSQQQQLLQDLQVEEHVSTQNYVMI
          ATLTVEQLSSRVSFTSLSDDTSTADSLEPSAQQPSQQQQLLQDLQVEE.VSTQNYVMI
Retrocopy ATLTVEQLSSRVSFTSLSDDTSTADSLEPSAQQPSQQQQLLQDLQVEEQVSTQNYVMI

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	1.68 RPM
SRP007412_cerebellum	0.00 RPM	2.00 RPM
SRP007412_heart	0.00 RPM	0.56 RPM
SRP007412_kidney	0.04 RPM	1.19 RPM
SRP007412_liver	0.00 RPM	0.49 RPM
SRP007412_testis	0.14 RPM	1.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1583 was not detected

EST

No EST(s) were mapped for retro_mmus_1583 retrocopy.

TSS

No TSS is located nearby retro_mmus_1583 retrocopy 5' end.

Lab

retro_mmus_1583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1583 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012559	1 retrocopy	retro_chof_263,
Mus musculus	ENSMUSG00000029638	1 retrocopy	retro_mmus_1583 ,