RetrogeneDB ID: retro_mmus_1904

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:36909195..36909587(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081591
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Btf3
• Ensembl ID: ENSMUSG00000021660
• Aliases: Btf3, 1700054E11Rik
• Description: basic transcription factor 3 [Source:MGI Symbol;Acc:MGI:1202875]

Sequence

>retro_mmus_1904
GTATTTCACAGAACAGCCACAGCAGACCATAAAAAAAATGCAGTTCTCCTTAAAGAAGTTAGGGGTAAACAATGTCTCTG
GTATTGAAGAGGTAAATATGTTTACAAACCAGAGAACAGTGACCCATTTTAATGACCCTAAAGTTCAGGCATCTCTGGCA
TCAAACGCCTTCACCATTGCAGGCCACGCTGAGACGAAGCAGCTGACAGAAATGCTTCCCAGCATCCTAAACCAGCTCGG
TGCAGACAATCTGACTAGTTTAAGGAGACTGGCTGATACTCTGCCCAAACAATCTGTGGATGGAAAGCACCACTTGTTTC
TGGAGATGCAGATGAAGATGAAGTTCCAGATATGGGGAGAATTTTGATGAGGCTTCTAAGAATGCAGCACAC

Alignment

ORF - retro_mmus_1904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.85 %
• Parental protein coverage: 80.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVHRTATADDKKL-QFSLKKLGVNNISGIEEVNMFTNQGTVIHFNNPKVQASLAANTFTITGHAETKQLT
          V.HRTATAD.....QFSLKKLGVNN.SGIEEVNMFTNQ.TV.HFN.PKVQASLA.N.FTI.GHAETKQLT
Retrocopy VFHRTATADHXXX>QFSLKKLGVNNVSGIEEVNMFTNQRTVTHFNDPKVQASLASNAFTIAGHAETKQLT

Parental  EMLPSILNQLGADSLTSLRRLAEALPKQSVDG-KAPLATGEDDDDEVPDL-VENFDEASKNEAN
          EMLPSILNQLGAD.LTSLRRLA..LPKQSVDG.KAPL..G..D.DEVPD...ENFDEASKN.A.
Retrocopy EMLPSILNQLGADNLTSLRRLADTLPKQSVDG<KAPLVSGDADEDEVPDM<GENFDEASKNAAH

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	31.21 RPM
SRP007412_cerebellum	0.00 RPM	33.00 RPM
SRP007412_heart	0.00 RPM	33.90 RPM
SRP007412_kidney	0.00 RPM	50.80 RPM
SRP007412_liver	0.00 RPM	44.76 RPM
SRP007412_testis	0.00 RPM	108.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1904 was not detected

EST

No EST(s) were mapped for retro_mmus_1904 retrocopy.

TSS

No TSS is located nearby retro_mmus_1904 retrocopy 5' end.

Lab

retro_mmus_1904 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1904 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 154 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011563	14 retrocopies	retro_amel_1257, retro_amel_1279, retro_amel_1324, retro_amel_1334, retro_amel_1433, retro_amel_166, retro_amel_1769, retro_amel_182, retro_amel_1841, retro_amel_480, retro_amel_513, retro_amel_784, retro_amel_908, retro_amel_986,
Choloepus hoffmanni	ENSCHOG00000001861	13 retrocopies	retro_chof_1027, retro_chof_1166, retro_chof_117, retro_chof_1397, retro_chof_1406, retro_chof_1884, retro_chof_1960, retro_chof_2194, retro_chof_2682, retro_chof_2703, retro_chof_344, retro_chof_364, retro_chof_700,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Cavia porcellus	ENSCPOG00000012832	1 retrocopy	retro_cpor_81,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Dasypus novemcinctus	ENSDNOG00000018682	4 retrocopies	retro_dnov_1958, retro_dnov_2107, retro_dnov_497, retro_dnov_817,
Felis catus	ENSFCAG00000023973	10 retrocopies	retro_fcat_1044, retro_fcat_1378, retro_fcat_1438, retro_fcat_187, retro_fcat_188, retro_fcat_225, retro_fcat_28, retro_fcat_419, retro_fcat_593, retro_fcat_919,
Homo sapiens	ENSG00000145741	11 retrocopies	retro_hsap_1215, retro_hsap_1396, retro_hsap_2259, retro_hsap_2525, retro_hsap_2819, retro_hsap_2964, retro_hsap_3533, retro_hsap_3551, retro_hsap_3972, retro_hsap_4270, retro_hsap_625,
Myotis lucifugus	ENSMLUG00000012912	11 retrocopies	retro_mluc_1024, retro_mluc_1349, retro_mluc_1459, retro_mluc_1748, retro_mluc_1820, retro_mluc_1823, retro_mluc_2560, retro_mluc_2602, retro_mluc_482, retro_mluc_682, retro_mluc_694,
Macaca mulatta	ENSMMUG00000022291	2 retrocopies	retro_mmul_105, retro_mmul_2424,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Mustela putorius furo	ENSMPUG00000005864	28 retrocopies	retro_mputfur_1125, retro_mputfur_1149, retro_mputfur_1267, retro_mputfur_1289, retro_mputfur_1319, retro_mputfur_1321, retro_mputfur_1386, retro_mputfur_1414, retro_mputfur_1472, retro_mputfur_1525, retro_mputfur_1548, retro_mputfur_1576, retro_mputfur_1599, retro_mputfur_246, retro_mputfur_324, retro_mputfur_392, retro_mputfur_403, retro_mputfur_431, retro_mputfur_618, retro_mputfur_661, retro_mputfur_724, retro_mputfur_728, retro_mputfur_753, retro_mputfur_760, retro_mputfur_795, retro_mputfur_901, retro_mputfur_926, retro_mputfur_972,
Mus musculus	ENSMUSG00000021660	11 retrocopies	retro_mmus_1904 , retro_mmus_2445, retro_mmus_2769, retro_mmus_3054, retro_mmus_3272, retro_mmus_3344, retro_mmus_3525, retro_mmus_443, retro_mmus_451, retro_mmus_470, retro_mmus_707,
Mus musculus	ENSMUSG00000028568	2 retrocopies	retro_mmus_1134, retro_mmus_2743,
Pan troglodytes	ENSPTRG00000016979	12 retrocopies	retro_ptro_1470, retro_ptro_1599, retro_ptro_1675, retro_ptro_1912, retro_ptro_2006, retro_ptro_2413, retro_ptro_2494, retro_ptro_2697, retro_ptro_2896, retro_ptro_455, retro_ptro_832, retro_ptro_959,
Pteropus vampyrus	ENSPVAG00000007160	11 retrocopies	retro_pvam_1011, retro_pvam_241, retro_pvam_301, retro_pvam_440, retro_pvam_456, retro_pvam_515, retro_pvam_602, retro_pvam_647, retro_pvam_70, retro_pvam_882, retro_pvam_919,
Sorex araneus	ENSSARG00000007736	5 retrocopies	retro_sara_195, retro_sara_279, retro_sara_354, retro_sara_427, retro_sara_74,
Tarsius syrichta	ENSTSYG00000001295	7 retrocopies	retro_tsyr_1360, retro_tsyr_1388, retro_tsyr_212, retro_tsyr_707, retro_tsyr_878, retro_tsyr_90, retro_tsyr_954,
Tursiops truncatus	ENSTTRG00000007290	2 retrocopies	retro_ttru_1883, retro_ttru_391,
Vicugna pacos	ENSVPAG00000009607	2 retrocopies	retro_vpac_185, retro_vpac_467,