RetrogeneDB ID: retro_rnor_960

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:48503142..48504488(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000021438
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_960
CTAAATACGTGCATCTCCATCCACATTGGTCATGCTGGTGTCCAGGTCAGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACATGGCATCCAGCCTGATGGCCAGATGCCAAGCGACAAGACCATTGGGAGAGGAGATGACTCCCTCAACACCTTCTTCA
GTGAGACAGGAGCTGGCAAGCACGTGCCCCGGGCAGTGTTTGTAGACCTGGAACCCACAGGTATTGATGAAGTTCGCACT
GGTACCTACCGCCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCTGTGGCCA
CTACACCATTGGCAAGGAGATCACTGACCTTGTCGTGGACAGAATTCACAAGCTGGCTGACCAGTGCACGGATCTCCAGG
GCTTCTTGGTTTTCCACAGCTTTGGTGGGAGAACTGGCTTTGGGTTCACCTCCCTACTGATGGAGCGGCTCTGTGTGGAT
TACAGAAAGAAGTCCAAGCTGGTGTTCTCCATTTACCCAACCCCCAGGGTTCTACTGCTGTGGCTGAGCCCTACAATTCC
ATCCGCATCACTCATACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGTCCATCTATGACATCTGTTG
TAGAAACTTCAATACTGAGCACCCAACCTACACTAACCTTAACTGTGTTATTAGCCAGATTGTGTCTTCCATCACTGCTT
CCCTCAGACTTAATGGGGTCCTGAATGTTGATCTGACAGAATTCCAGACCAACCTACTGCCCTATCCTTGCATCCACTTC
CCTCTGGCCACTTATGCTCTTTTCGTCTCTGCTGAAAAAGCCTACCATGAGCAACTTATAGTAGCAGAGATCACCAATGC
CTGTTTTGAGCCAACTAACCAGATGGTGAAATGTGACCCTGGCCATGGTAAATACATGGTTTGCTGCCTGCTGTACCATG
GTGATGTGGTTCCCAAGGAAGTCAATCCCGCCATTGCCACCATCAAGACCAAGCACACCATCCAGTTTGTGGACTGGTGC
ACCACTGGCTTCAAGGTTGTCACTAATTACCAGCCTCCCACTGTGGTACTTGGTGGTGATCTGGCCAGGGTTCAGAGAGC
TGTGTGCATGTTGAGCAACACCACAGCCATTGCTAAGGCCTGGGCTTGCCTAGATCATAAGTTTGATCTGATGTATGCCA
AACATGCCTTTGTGCACTGGTATGTGGGTGAGGGCATGAAGGAGGGAGAGTTCTCTGAGGACCGTGAAGATATGGCTGCC
CTAGAGAAGGATTATGAGGAGATTGGGTCAGATAGTGCTGAAGGAGACGATGAAGGTGAAAAATAT

Alignment

ORF - retro_rnor_960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          ...CISIH.G.AGVQ..NACWELYCLEHGIQPDGQMPSDKTIG.GDDS.NTFFSETGAGKHVPRAVFVDL
Retrocopy LNTCISIHIGHAGVQVSNACWELYCLEHGIQPDGQMPSDKTIGRGDDSLNTFFSETGAGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EPT.IDEVRTGTYRQLFHPEQLITGKEDAANNYA.GHYTIGKEI.DLV.DRI.KLADQCT.LQGFLVFHS
Retrocopy EPTGIDEVRTGTYRQLFHPEQLITGKEDAANNYACGHYTIGKEITDLVVDRIHKLADQCTDLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQV-STAVVEPYNSILTTHTTLEHSDCAFMVDNEAI
          FGG.TG.GFTSLLMERL.VDY.KKSKL.FSIYP.P.V.STAV.EPYNSI..THTTLEHSDCAFMVDNE.I
Retrocopy FGGRTGFGFTSLLMERLCVDYRKKSKLVFSIYPTPRV<STAVAEPYNSIRITHTTLEHSDCAFMVDNESI

Parental  YDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAE
          YDIC.RN...E.PTYTNLN..ISQIVSSITASLR..G.LNVDLTEFQTNL.PYP.IHFPLATYA...SAE
Retrocopy YDICCRNFNTEHPTYTNLNCVISQIVSSITASLRLNGVLNVDLTEFQTNLLPYPCIHFPLATYALFVSAE

Parental  KAYHEQLTVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPT
          KAYHEQL.VAEITNACFEP.NQMVKCDP.HGKYM.CCLLY.GDVVPK.VN.AIATIKTK.TIQFVDWC.T
Retrocopy KAYHEQLIVAEITNACFEPTNQMVKCDPGHGKYMVCCLLYHGDVVPKEVNPAIATIKTKHTIQFVDWCTT

Parental  GFKVGINYQPPTVVPGGDLARVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFS
          GFKV..NYQPPTVV.GGDLARVQRAVCMLSNTTAIA.AWA.LDHKFDLMYAK.AFVHWYVGEGM.EGEFS
Retrocopy GFKVVTNYQPPTVVLGGDLARVQRAVCMLSNTTAIAKAWACLDHKFDLMYAKHAFVHWYVGEGMKEGEFS

Parental  EAREDMAALEKDYEEVGADSAEGDDEGEEY
          E.REDMAALEKDYEE.G.DSAEGDDEGE.Y
Retrocopy EDREDMAALEKDYEEIGSDSAEGDDEGEKY

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	29.84 RPM
SRP017611_kidney	0.07 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_960 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_960 has 0 orthologous retrocopies within eutheria group .

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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 ,