RetrogeneDB ID: retro_rnor_1841

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:154572834..154573368(+)
• Located in intron of: ENSRNOG00000007738

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mcts1
• Ensembl ID: ENSRNOG00000002563
• Aliases: None
• Description: Malignant T-cell-amplified sequence 1 [Source:UniProtKB/Swiss-Prot;Acc:Q4G009]

Sequence

>retro_rnor_1841
AAATTTGACGAGAAAGAAAGTGTGTCCAACTGCATCCAACTGAAAACTTCCGTTATTAAGGGTATTAAGAGCCAACTGAC
TGAGCAGTTTCCAGGTATCGAGCCGTGGCTTAATCAAATCATGCCTAAGAAAGATCCCGTCAAAATAGTGAGATGCCATG
AACACATGGAAATCCTTACAGTCAACGGAGAATTACTGTTTTTCAGGCAGAGAAAAGGACCTTTTTATCCAACGCTAAGA
TTACTTCACAAATACCCGTTTATCCTGCCACACCAGCAGGTCGACAAAGGAGCCATCAAATTTGTGCTCAGTGGTGCAAA
TATCATGTGTCCGGGTTTAACATCTCCTGGAGCGAAGCTCTACACTGCTGCAGTAGATACCATCGTGGCGGTCATGGCAG
AAGGGAAAGAGCATGCCCTGTGTGTCGGAGTCATGAAGATGGCAGCAGCAGACATTGAGAAGATCAACAAGGGGATCGGC
ATTGAGAATATCCATTATCTAAATGACGGGCTGTGGCACATGAAGACATATAAG

Alignment

ORF - retro_rnor_1841 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 97.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RFDEKENVSNCIQLKTSVIKGIKNQLLEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLFFRQ
          .FDEKE.VSNCIQLKTSVIKGIK.QL.EQFPGIEPWLNQIMPKKDPVKIVRCHEH.EILTVNGELLFFRQ
Retrocopy KFDEKESVSNCIQLKTSVIKGIKSQLTEQFPGIEPWLNQIMPKKDPVKIVRCHEHMEILTVNGELLFFRQ

Parental  REGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAIMAEGKQHAL
          R.GPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLY.AAVDTIVA.MAEGK.HAL
Retrocopy RKGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYTAAVDTIVAVMAEGKEHAL

Parental  CVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          CVGVMKM.A.DIEK.NKGIGIENIHYLNDGLWHMKTYK
Retrocopy CVGVMKMAAADIEKINKGIGIENIHYLNDGLWHMKTYK

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	5.18 RPM	18.05 RPM
SRP017611_kidney	6.70 RPM	15.70 RPM
SRP017611_liver	2.69 RPM	14.73 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1841 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1841 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1841 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2422
Pan troglodytes	retro_ptro_1396
Gorilla gorilla	retro_ggor_1507
Pongo abelii	retro_pabe_1786
Macaca mulatta	retro_mmul_626
Mus musculus	retro_mmus_69

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Erinaceus europaeus	ENSEEUG00000007258	1 retrocopy	retro_eeur_197,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Homo sapiens	ENSG00000232119	1 retrocopy	retro_hsap_2422,
Gorilla gorilla	ENSGGOG00000009420	1 retrocopy	retro_ggor_1507,
Myotis lucifugus	ENSMLUG00000015101	1 retrocopy	retro_mluc_16,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pan troglodytes	ENSPTRG00000022241	1 retrocopy	retro_ptro_1396,
Pteropus vampyrus	ENSPVAG00000013249	3 retrocopies	retro_pvam_1323, retro_pvam_645, retro_pvam_867,
Rattus norvegicus	ENSRNOG00000002563	2 retrocopies	retro_rnor_1841 , retro_rnor_957,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Tupaia belangeri	ENSTBEG00000010666	2 retrocopies	retro_tbel_1485, retro_tbel_4265,
Tarsius syrichta	ENSTSYG00000001440	1 retrocopy	retro_tsyr_55,
Tursiops truncatus	ENSTTRG00000007208	1 retrocopy	retro_ttru_1587,