RetrogeneDB ID: retro_mmus_1279

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:53172729..53173590(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000096662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nrbf2
• Ensembl ID: ENSMUSG00000075000
• Aliases: Nrbf2, NRBF-2
• Description: nuclear receptor binding factor 2 [Source:MGI Symbol;Acc:MGI:1354950]

Sequence

>retro_mmus_1279
ATGGAAGTGATGGAAGGACCCCTCAACCTTGCTCACCAACAGAGCCGCCGAGCAGACCGTTTGTTAGCTGCTGGGAAATA
CGAAGAGGCGATTTCTTGTCACAGAAAGGCAACAACATATCTCTCTGAAGCCATGAAGCTGACCGAGTCTGAGCAGGCTC
ACTTATCACTGGAACTGCAAAGGGACAGCCACATGAAACAGCTTCTTCTCATCCAGGAGAGGTGGAAGAGAGCAAAGCGA
GAGGAGCGGTTGAAAGCGCAGCAGAGCACGGAACGAGATGGAGCCCCCCACCTGCAGGCACCTCCCAGGCCCTCTGAGGA
TGCTGAAGGCCAGAGCCCTCTGCTTTCTCAGCCATACATCCCTTCCACAGAGAGGCGCCTCCCCGAGGTGCAGGGGGTCT
TTGACAGGGATCCAGACACATTGTTGTTTTTACTTCAGCAAAAGAATGAGCCATCAGAGCCTTGTATTGGAAGCAAAGCC
CCAAAAGATGATAAAACGATTATAGAGGAGCAGGCAACCAAAATAGCAGATTTGAAGAGGCATGTGGAGTTCCTTGTGGC
TGAGAATGAAAGATTAAGGAAAGAAAATAAACAGCTAAAGGCTGAAAAGGCCAGACTCCTGAAAGGCACAGCTGAGAAGG
AACTGGACGTCGATGCAGACTTTGTAGAGAAGTCAGAGCTGTGGGGCTTACCTTCACACTCGGAATCCGCCGCTGCCTCT
TCAACCTGGCAGAAGTTTGCAGCTAACACGGGGAAAGCCAAGGACATTCCAATACCCAACCTCCCTCCTCTGGATTTCCC
ATCTCCAGAGCTTCCTCTGATGGAGCTCTCGGAGGACATTCTGAAAGGATTCATGACTGAC

Alignment

ORF - retro_mmus_1279 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHRKATTYLSEAMKLTESEQAHLSLELQRDSHMKQLLL
          MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHRKATTYLSEAMKLTESEQAHLSLELQRDSHMKQLLL
Retrocopy MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHRKATTYLSEAMKLTESEQAHLSLELQRDSHMKQLLL

Parental  IQERWKRAKREERLKAQQSTERDGAPHLQAPPRPSEDAEGQSPLLSQPYIPSTERRLPEVQGVFDRDPDT
          IQERWKRAKREERLKAQQSTERDGAPHLQAPPRPSEDAEGQSPLLSQPYIPSTERRLPEVQGVFDRDPDT
Retrocopy IQERWKRAKREERLKAQQSTERDGAPHLQAPPRPSEDAEGQSPLLSQPYIPSTERRLPEVQGVFDRDPDT

Parental  LLFLLQQKNEPSEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGT
          LLFLLQQKNEPSEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGT
Retrocopy LLFLLQQKNEPSEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGT

Parental  AEKELDVDADFVEKSELWGLPSHSESAAASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDI
          AEKELDVDADFVEKSELWGLPSHSESAAASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDI
Retrocopy AEKELDVDADFVEKSELWGLPSHSESAAASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDI

Parental  LKGFMND
          LKGFM.D
Retrocopy LKGFMTD

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	4.93 RPM
SRP007412_cerebellum	0.00 RPM	3.21 RPM
SRP007412_heart	0.00 RPM	3.21 RPM
SRP007412_kidney	0.00 RPM	3.46 RPM
SRP007412_liver	0.00 RPM	5.73 RPM
SRP007412_testis	0.00 RPM	1.05 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1279 was not detected

EST

No EST(s) were mapped for retro_mmus_1279 retrocopy.

TSS

No TSS is located nearby retro_mmus_1279 retrocopy 5' end.

Lab

retro_mmus_1279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1279 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004648	3 retrocopies	retro_chof_1032, retro_chof_2250, retro_chof_2568,
Homo sapiens	ENSG00000148572	3 retrocopies	retro_hsap_2643, retro_hsap_3999, retro_hsap_433,
Gorilla gorilla	ENSGGOG00000013016	2 retrocopies	retro_ggor_1846, retro_ggor_2685,
Macropus eugenii	ENSMEUG00000010849	3 retrocopies	retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta	ENSMMUG00000017726	1 retrocopy	retro_mmul_1523,
Monodelphis domestica	ENSMODG00000017183	1 retrocopy	retro_mdom_1995,
Mus musculus	ENSMUSG00000075000	2 retrocopies	retro_mmus_1278, retro_mmus_1279 ,
Otolemur garnettii	ENSOGAG00000005856	1 retrocopy	retro_ogar_2110,
Pongo abelii	ENSPPYG00000002411	3 retrocopies	retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes	ENSPTRG00000002539	3 retrocopies	retro_ptro_1780, retro_ptro_194, retro_ptro_2715,
Rattus norvegicus	ENSRNOG00000000641	2 retrocopies	retro_rnor_1681, retro_rnor_994,
Sarcophilus harrisii	ENSSHAG00000004744	1 retrocopy	retro_shar_427,
Ictidomys tridecemlineatus	ENSSTOG00000011341	1 retrocopy	retro_itri_183,