RetrogeneDB ID: retro_rnor_876

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:36786100..36786676(+)
• Located in intron of: ENSRNOG00000046100

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000049404
• Aliases: None
• Description: None

Sequence

>retro_rnor_876
AGCATGTTCTGTGTACAGAAGAGCCTTGCCTCTAGTGTCCTCCACTGTGCTAAAAAGAAGGTCCACTTGGACCCCAATGA
CACCGATAAAATCGCCAATGCCAACGCCCGTCAGCTGATCAGGAAGCTGATTGAAGATGGCCTGATCATCTGGAAGACTG
TAACTGTCCATCCTCAGACTCGCTGCCTAAAATCACCTTGAAGGGCAGGCATATGGTCATAGGGAAGGGAAAGGGTACTG
CCAACACTTGGGTTCCTGAGAGGGTAACGTGGATGAGAAGGATGAGAATCCTGCACCGGCTTCTCAGGAGATACTGGGAA
TCTAAGAAGATTGACCACCATATGTATCACAGCCTGTACCTGTAGGTCAAAAGGAATGTATTCAAAAACCAATGGATTCT
TATGGAGCAGATCCTCAAACCGAAGGCAGACAAGGCCTGCAAGAAGCTACTGGCTGACCAGAATGAAGCTCACAGTTCTA
ATACCAAGGCAGCACAAAAACGCGTGGGAGAAGGGCCTCCAGGCCAAGAAGGAGGAGATCATCAATACTCTGTCCAAGGA
GGAAGAGACCCAGAAA

Alignment

ORF - retro_rnor_876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.75 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SMFGLQKCLASSFLHCAKKKVHLDPNETDKIANANARQLIRKLIEDGLIIWKPVTVHPQTRCLKT-LKG-
          SMF..QK.LASS.LHCAKKKVHLDPN.TDKIANANARQLIRKLIEDGLIIWK.VTVHPQTRCLK..L.G.
Retrocopy SMFCVQKSLASSVLHCAKKKVHLDPNDTDKIANANARQLIRKLIEDGLIIWKTVTVHPQTRCLKS>LEG>

Parental  RHMVIGKGKGTANTWVPERVTWMRRMRILHRLLRRYWESKKIDHHMYHSLYLKVKRNVFKNQWILMEQIL
          RHMVIGKGKGTANTWVPERVTWMRRMRILHRLLRRYWESKKIDHHMYHSLYL.VKRNVFKNQWILMEQIL
Retrocopy RHMVIGKGKGTANTWVPERVTWMRRMRILHRLLRRYWESKKIDHHMYHSLYL*VKRNVFKNQWILMEQIL

Parental  KPKADKACKKLLADQDEAHSTNTKAAQKR-EEG-LQAKKEEIINTLSKEEETQK
          KPKADKACKKLLADQ.EAHS.NTKAAQKR..EG.LQAKKEEIINTLSKEEETQK
Retrocopy KPKADKACKKLLADQNEAHSSNTKAAQKRVGEG>LQAKKEEIINTLSKEEETQK

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_876 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_876 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000004741	37 retrocopies	retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Rattus norvegicus	ENSRNOG00000049404	12 retrocopies	retro_rnor_1096, retro_rnor_1097, retro_rnor_1553, retro_rnor_1554, retro_rnor_1555, retro_rnor_1810, retro_rnor_202, retro_rnor_2054, retro_rnor_2530, retro_rnor_466, retro_rnor_511, retro_rnor_876 ,