RetrogeneDB ID: retro_rnor_1149

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:41556704..41557079(-)
• Located in intron of: ENSRNOG00000009278

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nutf2
• Ensembl ID: ENSRNOG00000018945
• Aliases: Nutf2, NTF2
• Description: Nuclear transport factor 2 [Source:UniProtKB/Swiss-Prot;Acc:P61972]

Sequence

>retro_rnor_1149
ATGGGAGACAAGCCAATTTGGGAGCAGATTGGATCCAGCTTTATTCAGAATTACTATCCATTATTTGATAACGACAGAAC
CCAACTAGGAGCAATTTACATTGGTGCATCATGCCTTACGTGGGAAGGACAGCAATTCCAGGGCAAAGCTGCCATTGTGG
AGAAGTTATCTAGTCTTCCGTTCCAGAAAATTCAGCATAGTATCATGGCACAGCAGTATCAGCCTACACCAGATAGCTGC
ATCATCAGCATGGTTGTAGGCCAGCTCAAGGCTGATGAAGATCCCATCATGGGTTTCCACCAGATGTTTCTATTAAAGAA
CATCAATGATGCTTGGGTTTGCACCAATGACATGTTCAGGCTTGCCCTGCACAAC

Alignment

ORF - retro_rnor_1149 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.2 %
• Parental protein coverage: 98.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITA
          MGDKPIWEQIGSSFIQ.YY.LFDNDRTQLGAIYI.ASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSI.A
Retrocopy MGDKPIWEQIGSSFIQNYYPLFDNDRTQLGAIYIGASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSIMA

Parental  QDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHN
          Q..QPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHN
Retrocopy QQYQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHN

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	0.14 RPM	36.74 RPM
SRP017611_kidney	0.14 RPM	35.45 RPM
SRP017611_liver	0.00 RPM	16.74 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1149 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1149 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1149 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017548	5 retrocopies	retro_amel_1225, retro_amel_134, retro_amel_1485, retro_amel_415, retro_amel_445,
Bos taurus	ENSBTAG00000006414	2 retrocopies	retro_btau_1573, retro_btau_881,
Cavia porcellus	ENSCPOG00000003521	1 retrocopy	retro_cpor_1368,
Erinaceus europaeus	ENSEEUG00000003470	2 retrocopies	retro_eeur_149, retro_eeur_571,
Gorilla gorilla	ENSGGOG00000023925	5 retrocopies	retro_ggor_1032, retro_ggor_2152, retro_ggor_279, retro_ggor_2806, retro_ggor_3028,
Macropus eugenii	ENSMEUG00000009874	11 retrocopies	retro_meug_1023, retro_meug_136, retro_meug_1539, retro_meug_1585, retro_meug_1778, retro_meug_2140, retro_meug_253, retro_meug_282, retro_meug_352, retro_meug_676, retro_meug_748,
Myotis lucifugus	ENSMLUG00000025175	3 retrocopies	retro_mluc_1265, retro_mluc_2194, retro_mluc_911,
Macaca mulatta	ENSMMUG00000012038	6 retrocopies	retro_mmul_1160, retro_mmul_1270, retro_mmul_2127, retro_mmul_2169, retro_mmul_2593, retro_mmul_27,
Monodelphis domestica	ENSMODG00000005517	6 retrocopies	retro_mdom_1031, retro_mdom_1291, retro_mdom_1488, retro_mdom_1489, retro_mdom_1903, retro_mdom_37,
Mus musculus	ENSMUSG00000008450	1 retrocopy	retro_mmus_232,
Oryctolagus cuniculus	ENSOCUG00000006322	1 retrocopy	retro_ocun_115,
Otolemur garnettii	ENSOGAG00000015568	2 retrocopies	retro_ogar_2713, retro_ogar_2811,
Rattus norvegicus	ENSRNOG00000018945	4 retrocopies	retro_rnor_1149 , retro_rnor_1616, retro_rnor_2427, retro_rnor_545,
Sarcophilus harrisii	ENSSHAG00000006100	1 retrocopy	retro_shar_274,
Sus scrofa	ENSSSCG00000030295	3 retrocopies	retro_sscr_1223, retro_sscr_710, retro_sscr_740,
Tupaia belangeri	ENSTBEG00000011016	1 retrocopy	retro_tbel_7,
Tursiops truncatus	ENSTTRG00000009251	2 retrocopies	retro_ttru_1534, retro_ttru_433,
Drosophila melanogaster	FBgn0031145	1 retrocopy	retro_dmel_27,