RetrogeneDB ID: retro_mmus_3243

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:4978374..4979175(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tfdp1
• Ensembl ID: ENSMUSG00000038482
• Aliases: Tfdp1, Dp1, Drtf1
• Description: transcription factor Dp 1 [Source:MGI Symbol;Acc:MGI:101934]

Sequence

>retro_mmus_3243
CTGGTGGCAGAGTTCAGCGCTGCCGGCATCCTGCCAAACAAATCAGCTTATGACCAGAAGAACATCCGGCGGCGTGTCTA
CGATGCCTTAAATGTGCTAATGGCCATGAACATCATCTCCAAGGAGAAGAAGGAGATCAAATGGATCGGCCTGCCCACCA
ACTCAGCTCAGGAGTGCCAGAACTTAGAGGTAGAGAGGCAGCGGAGGCTGGAGAGGATCAAACAGAAGCAGTCACAGCTC
CAGGAGCTCATCCTGCAGCAAATTGCCTTCAAGAACTTGGTGCAGAGAAATCGCCAAGCTGAGCAGCAGGCCCGCAGGCC
GCCTCTTCCCAACTCTGTCATCCACTTGCCCTTCATCATTGTCAACACCAGCAGGAAGACAGTCATTGACTGCAGCATCT
CCTATGATAAATTTGAGTATCTGTTTAACTTTGACAACGCCTTTGAGATCCACGATGACATTGAGGTGCTCAAGCGCATG
GGCATGGCATGTGGGCTGGAGTCTGGCAACTGCTCTGCTGAAGACCTCAAGGTGGCCAGAAGTTTGGTACCAAAAGCTCT
AGAACCATACGTGACAGAAATGGCTCAGGGATCCACTGGTGGAGTATTCGTCACGACAACAGGTTCTACATCCAATGGCA
CAAGGCTTTCTGCCAGTGATTTGAGCAATGGTGCAGATGGGATGCTGGCCACGAGCTCCAATGGGTCTCAGTACAGCGGC
TCCAGGGTCGAGACCCCTGTGTCCTACGTTGGGGAGGATGATGACGACGATGATGACTTTAATGAGAACGACGAGGAGGA
T

Alignment

ORF - retro_mmus_3243 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.03 %
• Parental protein coverage: 65.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVAEFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQR
          LVAEFSAA...ILPN.SAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQR
Retrocopy LVAEFSAAG--ILPNKSAYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQR

Parental  RLERIKQKQSQLQELILQQIAFKNLVQRNRQAEQQARRPPPPNSVIHLPFIIVNTSRKTVIDCSISNDKF
          RLERIKQKQSQLQELILQQIAFKNLVQRNRQAEQQARRPP.PNSVIHLPFIIVNTSRKTVIDCSIS.DKF
Retrocopy RLERIKQKQSQLQELILQQIAFKNLVQRNRQAEQQARRPPLPNSVIHLPFIIVNTSRKTVIDCSISYDKF

Parental  EYLFNFDNTFEIHDDIEVLKRMGMACGLESGNCSAEDLKVARSLVPKALEPYVTEMAQGSIGGVFVTTTG
          EYLFNFDN.FEIHDDIEVLKRMGMACGLESGNCSAEDLKVARSLVPKALEPYVTEMAQGS.GGVFVTTTG
Retrocopy EYLFNFDNAFEIHDDIEVLKRMGMACGLESGNCSAEDLKVARSLVPKALEPYVTEMAQGSTGGVFVTTTG

Parental  STSNGTRLSASDLSNGADGMLATSSNGSQYSGSRVETPVSYVGEDDDDDDDFNENDEED
          STSNGTRLSASDLSNGADGMLATSSNGSQYSGSRVETPVSYVGEDDDDDDDFNENDEED
Retrocopy STSNGTRLSASDLSNGADGMLATSSNGSQYSGSRVETPVSYVGEDDDDDDDFNENDEED

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	0.05 RPM	24.74 RPM
SRP007412_cerebellum	0.00 RPM	24.45 RPM
SRP007412_heart	0.03 RPM	14.88 RPM
SRP007412_kidney	0.00 RPM	15.13 RPM
SRP007412_liver	0.00 RPM	12.32 RPM
SRP007412_testis	0.14 RPM	27.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3243 was not detected

EST

No EST(s) were mapped for retro_mmus_3243 retrocopy.

TSS

No TSS is located nearby retro_mmus_3243 retrocopy 5' end.

Lab

retro_mmus_3243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3243 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243 , retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132, retro_pabe_378,