RetrogeneDB ID: retro_rnor_836

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:70018467..70018943(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Btf3
• Ensembl ID: ENSRNOG00000016912
• Aliases: None
• Description: transcription factor BTF3 [Source:RefSeq peptide;Acc:NP_001008310]

Sequence

>retro_rnor_836
ATGAAAGAAACGATCATGAACCAGGAAAACTCGCCCAGTGCAGGCACAAATGCGCGTTGGTGGGAAAGGAACTGCTCTTA
GAGAGAAGAAGGTAGTTCGCAGAACAGTCATGGCAGATGGTAAAAACCTGCAGTTCTCCACAAAGAAGTTAGGGCAAACA
ATATCTCTGGTGTTGAAGAGGTGAACATGTGTACAAACCAACACACCTAACAACCTAAAGTTCAGGCAACTCTAGCAGCG
AACACCTTCCCCGTTACAGGGCGCGCCGAGACAAAGTGGCTGACAGAAATGCTTCCCAGCATCTTCAACCAGCTTGGTGC
AGAACAGTCTGACTAGTTAGAGGAAACTGACTGAAGCTCTGCGTGAAAAGCAGATGGGTGGATGGAAAAGCACCACTTGC
TACTGGAGAGGATGATGATGATGAAGTTGCAGATCTAGTGGGGAATTTTGATTCAGCTTCTAAGACAGAAGCAAAC

Alignment

ORF - retro_rnor_836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MKETIMNQE-KLAK-LQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLG-VNNISGIEEVNMFTN
          MKETIMNQE.KLA...QAQ.R.GGKGTA.R.KKVV.RT..AD.K.LQFS.KKLG..NNISG.EEVNM.TN
Retrocopy MKETIMNQE<KLAQ<VQAQMRVGGKGTALREKKVVRRTVMADGKNLQFSTKKLG<ANNISGVEEVNMCTN

Parental  QGTVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSILNQLGAD-SLTSLRRLAEAL-PKQS-VDGKA
          Q....H...PKVQA.LAANTF..TG.AETK.LTEMLPSI.NQLGA..SLTS.R.L.EAL..KQ..VDGKA
Retrocopy Q----HT*QPKVQATLAANTFPVTGRAETKWLTEMLPSIFNQLGAE>SLTS*RKLTEALREKQM>VDGKA

Parental  PLATGEDDDDEVPDLVENFDEASKNEAN
          PLATGEDDDDEV.DLV.NFD.ASK.EAN
Retrocopy PLATGEDDDDEVADLVGNFDSASKTEAN

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
SRP017611_brain	0.00 RPM	39.83 RPM
SRP017611_kidney	0.07 RPM	93.58 RPM
SRP017611_liver	0.00 RPM	35.50 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_836 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_836 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010012	5 retrocopies	retro_btau_1161, retro_btau_1344, retro_btau_1361, retro_btau_459, retro_btau_551,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Equus caballus	ENSECAG00000021629	1 retrocopy	retro_ecab_200,
Echinops telfairi	ENSETEG00000017341	5 retrocopies	retro_etel_1216, retro_etel_1394, retro_etel_1997, retro_etel_405, retro_etel_960,
Gorilla gorilla	ENSGGOG00000000166	10 retrocopies	retro_ggor_1082, retro_ggor_1682, retro_ggor_1961, retro_ggor_2054, retro_ggor_2399, retro_ggor_2647, retro_ggor_2667, retro_ggor_548, retro_ggor_81, retro_ggor_946,
Microcebus murinus	ENSMICG00000017182	3 retrocopies	retro_mmur_1219, retro_mmur_1301, retro_mmur_651,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Nomascus leucogenys	ENSNLEG00000004718	9 retrocopies	retro_nleu_1081, retro_nleu_1199, retro_nleu_1284, retro_nleu_1446, retro_nleu_1797, retro_nleu_2526, retro_nleu_451, retro_nleu_496, retro_nleu_734,
Oryctolagus cuniculus	ENSOCUG00000024914	6 retrocopies	retro_ocun_1186, retro_ocun_1299, retro_ocun_1364, retro_ocun_446, retro_ocun_857, retro_ocun_916,
Pongo abelii	ENSPPYG00000029576	14 retrocopies	retro_pabe_1154, retro_pabe_1477, retro_pabe_180, retro_pabe_1885, retro_pabe_1956, retro_pabe_2207, retro_pabe_2458, retro_pabe_2918, retro_pabe_2919, retro_pabe_2932, retro_pabe_3329, retro_pabe_3484, retro_pabe_558, retro_pabe_649,
Rattus norvegicus	ENSRNOG00000008512	8 retrocopies	retro_rnor_1113, retro_rnor_1666, retro_rnor_1870, retro_rnor_1871, retro_rnor_1872, retro_rnor_537, retro_rnor_760, retro_rnor_998,
Rattus norvegicus	ENSRNOG00000016912	9 retrocopies	retro_rnor_187, retro_rnor_194, retro_rnor_2121, retro_rnor_2520, retro_rnor_2990, retro_rnor_2991, retro_rnor_2999, retro_rnor_836 , retro_rnor_953,