RetrogeneDB ID: retro_rnor_2260

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:148796805..148797735(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tuba1c
• Ensembl ID: ENSRNOG00000015544
• Aliases: None
• Description: Tubulin alpha-1C chain [Source:UniProtKB/Swiss-Prot;Acc:Q6AYZ1]

Sequence

>retro_rnor_2260
AGCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCAGTGAGACAGGAGCTGGCAAGCACGTGCCCCGGGCAGTGCT
CCTAGACCTGGAACCCACAGTTATTGATGAAGTTTGCACTGGCACCTAACGCCAGCTCTTCCACCCAGAGCAGCTCATCA
CAGGCAAGGAAGATGCTGCCAATAACTGTGCCCATGGCCACTACACCATTGGCAATGAGATCATTGACCTTGTCTTGGAC
AGAATTCGCAAGCTGGCTGGCCAGTTCACAGGTCTCCAGGGCTTTTTGGTTTTCCACAGCTTTGGTGGGGGAACCAGCTC
TGGGTTCACCTCGCTGCTGATGGAGCGGCTCTCTGTCGATTACAGGAAGGAGTCCAAGCTGGTGTTTTCCATTTACCCAG
CCCCCCGGGTTTCCACTGCTGTGGTTGAGCCCTACAATTCCATCCTCACCACCCACACCACCCTGGAGCCCTCTGATTGT
TCCTTCATGGTAGTCAATGAGGCCATCTCTGACATCTGTCATAGAAACCTCGACTTGGAGTGCTCAACCTACACTAACCT
TAACCGCCTTACTAGCCAGATTGTGTCTTCCATCACTGCTTCCCTCAGATTTGATGGGGCCCTGAATGTTGATCTGACAG
AATTCCAGACCAAGCTGGTGCCCTACCCTCGTATCCACTTCCCTCTGGCCACTTATGCCCCTGCCATCTCTGCTGAGAAA
GCCTACCATGAGCAGCTTTCTGTAGAGAGATCACCAATGCCTGCTTTGAGCCAGCCAACCAGATGTGACTCTTGCCATGG
TAAATACATGGCCCGCTGCCTGCTATACCATGATGATGTGATTCCCAAAGATGTCAATGCCTCCATTGCTACCATCAAGA
CCAAGCACAGCATCCAGTTTGTGGACTGGTGCCCCACTGGCTTCAAGTTG

Alignment

ORF - retro_rnor_2260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.07 %
• Parental protein coverage: 69.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTI
          .IGGGDDSFNTFFSETGAGKHVPRAV..DLEPTVIDEV.TGT.RQLFHPEQLITGKEDAANN.A.GHYTI
Retrocopy SIGGGDDSFNTFFSETGAGKHVPRAVLLDLEPTVIDEVCTGT*RQLFHPEQLITGKEDAANNCAHGHYTI

Parental  GKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
          G.EIIDLVLDRIRKLA.Q.TGLQGFLVFHSFGGGT.SGFTSLLMERLSVDY.K.SKL.FSIYPAP.VSTA
Retrocopy GNEIIDLVLDRIRKLAGQFTGLQGFLVFHSFGGGTSSGFTSLLMERLSVDYRKESKLVFSIYPAPRVSTA

Parental  VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNV
          VVEPYNSILTTHTTLE.SDC.FMV.NEAI.DIC.RNLD.E..TYTNLNRL.SQIVSSITASLRFDGALNV
Retrocopy VVEPYNSILTTHTTLEPSDCSFMVVNEAISDICHRNLDLECSTYTNLNRLTSQIVSSITASLRFDGALNV

Parental  DLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLTVAEITNACFEPANQMVKCDPRHGKYMACCLLYR
          DLTEFQT.LVPYPRIHFPLATYAP.ISAEKAYHEQL..............Q...CD..HGKYMA.CLLY.
Retrocopy DLTEFQTKLVPYPRIHFPLATYAPAISAEKAYHEQLS---VERSPMPALSQPTRCDSCHGKYMARCLLYH

Parental  GDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKV
          .DV.PKDVNA.IATIKTK..IQFVDWCPTGFK.
Retrocopy DDVIPKDVNASIATIKTKHSIQFVDWCPTGFKL

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	29.84 RPM
SRP017611_kidney	0.00 RPM	78.51 RPM
SRP017611_liver	0.00 RPM	32.81 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2260 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2260 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Rattus norvegicus	ENSRNOG00000015544	3 retrocopies	retro_rnor_1193, retro_rnor_2260 , retro_rnor_960,