RetrogeneDB ID: retro_rnor_867

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:20876952..20877879(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tubb4b
• Ensembl ID: ENSRNOG00000010170
• Aliases: Tubb4b, Tubb2, Tubb2c
• Description: tubulin beta-4B chain [Source:RefSeq peptide;Acc:NP_954525]

Sequence

>retro_rnor_867
ATGAGGGAGATCCTGCACCTGCAGGCTGCGCAGTGCGGCAACCAGATTGGCGCCAAGGTCTGGGAGGTAATCAGCGACGA
GCATGGCATTGATCCCACTGGCACGTACCACGGAGATAGCGACCTCTAGCTGGAGCGCATCAACGTGTACTACAACGAGG
CCACCGGTGGCAAGTATGTGCCCCGCGCTGTGCCCCTGGACTTGGAGCCCGGCACCATGGACTCGGTGCGCTCAGGGCCC
TTCGGGCAGATCTTCAGACCTGATAACTTCGTCTTTGGTCAGAGTGGGCTGGGAACAACTGAGCCAAGGGGCACTACACA
GAAGGTGCAGAGCTGGTTGACTCGGTGTTGGACGTTGTGACAAAGGAAGCTGAGAGCTGTGACTGCTTGCAGGGCTTCCA
GCTGACCCACTCCCTGGGTTGGGGGGACTGGGTCTGGGGTGGGTACCCTCCTTATCAGCAAGATCCCGGAGGAGTACCCA
GCCAGAATCTTGAACACCTTCAGTGTGGTCCCTTCCCCCAAGGTGTCGGACACAGTGGTTGAGCCCTACAATGACACCCT
TTCAGTCCACCAGCTTGTTGAAAACACAGATGAGACCTATTGTATTGATAACGAAGCACTCTATGACATCTGCTTCAGAA
CCCTAAAGCTGACCACACCCACTTATGGTGACCTGAACCATCTAGTGTCTGCCACCATGAGTGAGGTAACCACTTGCCTG
TGATTCTCTGGCCAGCTAAATGCTGACCTGCAGAAACTGGCTGTAAATACTCACCTGCACTTCTTCATGCCTGGTTTTGC
CCCCTTGACCAGCTGGGGAAGCCAGCAGTACCGTGCCCTGACAGTTCCTGAGCTCACCCAGCAGATGTTTGATGCCAAGA
ACATGATGGCTGCCTGTGATCCCCGCCATGGGCACTACTTGACAGTT

Alignment

ORF - retro_rnor_867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 70.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEP
          MREI.HLQA.QCGNQIGAK.WEVISDEHGIDPTGTYHGDSDL.LERINVYYNEATGGKYVPRAV..DLEP
Retrocopy MREILHLQAAQCGNQIGAKVWEVISDEHGIDPTGTYHGDSDL*LERINVYYNEATGGKYVPRAVPLDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSG-AGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          GTMDSVRSGPFGQIFRPDNFVFGQSG.AGNN.AKGHYTEGAELVDSVLDVV.KEAESCDCLQGFQLTHSL
Retrocopy GTMDSVRSGPFGQIFRPDNFVFGQSG<AGNN*AKGHYTEGAELVDSVLDVVTKEAESCDCLQGFQLTHSL

Parental  G-GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          G.GGTGSG.GTLLISKI.EEYP.RI.NTFSVVPSPKVSDTVVEPYN.TLSVHQLVENTDETYCIDNEALY
Retrocopy G>GGTGSGVGTLLISKIPEEYPARILNTFSVVPSPKVSDTVVEPYNDTLSVHQLVENTDETYCIDNEALY

Parental  DICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGS
          DICFRTLKLTTPTYGDLNHLVSATMS.VTTCL.F.GQLNADL.KLAVN......LHFFMPGFAPLTS.GS
Retrocopy DICFRTLKLTTPTYGDLNHLVSATMSEVTTCL*FSGQLNADLQKLAVN----THLHFFMPGFAPLTSWGS

Parental  QQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTV
          QQYRALTVPELTQQMFDAKNMMAACDPRHG.YLTV
Retrocopy QQYRALTVPELTQQMFDAKNMMAACDPRHGHYLTV

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	0.07 RPM	232.51 RPM
SRP017611_kidney	0.00 RPM	84.99 RPM
SRP017611_liver	0.00 RPM	62.19 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_867 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_867 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_867 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011966	1 retrocopy	retro_cpor_497,
Microcebus murinus	ENSMICG00000010939	1 retrocopy	retro_mmur_792,
Macaca mulatta	ENSMMUG00000012164	2 retrocopies	retro_mmul_1849, retro_mmul_2533,
Monodelphis domestica	ENSMODG00000017213	1 retrocopy	retro_mdom_117,
Mus musculus	ENSMUSG00000036752	2 retrocopies	retro_mmus_158, retro_mmus_422,
Otolemur garnettii	ENSOGAG00000005927	2 retrocopies	retro_ogar_3410, retro_ogar_3450,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,
Rattus norvegicus	ENSRNOG00000010170	2 retrocopies	retro_rnor_742, retro_rnor_867 ,