RetrogeneDB ID: retro_rnor_2819

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:74708456..74709367(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tuba4a
• Ensembl ID: ENSRNOG00000003597
• Aliases: Tuba4a, Tuba4
• Description: Tubulin alpha-4A chain [Source:UniProtKB/Swiss-Prot;Acc:Q5XIF6]

Sequence

>retro_rnor_2819
ATGTGTGAGTGAATTTCAGTCCATGTGGGACACGCTGGTGTCCAGATGGGCAATGCTTCCTGGGAGCTCTATTTTCTGGA
GCATGTGATTCAGCCTCATGGGCAGATGCAGAATCATAAGACCACTGGTTGAGTGGATGACTCCTTCACCACCTTCTTCT
GTGAAATGCAGCTGAAAAACATGTGCTTCAAGTGGTCTTTCTAGATCTGGAGCCTACTGTAGTGCATGAGACCTGAAATC
ACCCGAAATCTACATCTTCCACCCAGAGCAGCTTATCACTTAGAGAGAAGATGCAGTTCTTGACCATGCACTTGGCCACT
CCATTATTGGCAAGGGTATCATTACCCAGGGCATTACCAGACCCATAATCTATCTATTCAGTGTACAGGAATTCAGGGCT
TCCTATTGTTCCACAGCTTTGGAGGGGCCACCAGCTCAGTTTCATCCCTCAGTTGATGGGAGTACCTTTCTGTTAACCAT
AGCAAGAAGTCCTAGCTAGCAAGTGTTCTCCCTCCACCCAGCACAAGTGTCCAAGGCTGTGTGCACTACAACTCTATCCT
GAGCACAGTAACACCATGGAATGCTCAGATTGTGTCTTCATAGTAGACAATGAGGACAACTTTGACTTTTGCCATCACAA
CTGGGATATCGTGTGCCCAACCTATATAGATCGCAACTACCTTCTCAGCCAAATCAATGCCTCATCTCAGCTTCCTTCTG
CTCTGATGGGGCCTTCAATGTGGACATGACAGTGTTTCAGCGCAAACTGATTCCCTGCCCTCACATCCACTTCCTCTTGG
CCATCTATGCTCCATCATCTTGGCATAGAAGGTCTACCATGAACAGCTGCGAGTGGCAAGTTCACCATTGCCTGCTTTGA
GCCTGCCAACCAGACAGTGAACTGTGACCCT

Alignment

ORF - retro_rnor_2819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.6 %
• Parental protein coverage: 68.53 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCE-TGAGKHVPRAVFVD
          M.E.ISVHVG.AGVQMGNA.WELY.LEH.IQP.GQM...KT.G..DDSFTTFFCE...A.KHV...VF.D
Retrocopy MCE*ISVHVGHAGVQMGNASWELYFLEHVIQPHGQMQNHKTTG*VDDSFTTFFCE<NAAEKHVLQVVFLD

Parental  LEPTVIDEIRN-GPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDR-IRKLSDQCTGLQGFLV
          LEPTV..E..N..P....FHPEQLIT..EDA....A.GH..IGK.II.....R....LS.QCTG.QGFL.
Retrocopy LEPTVVHET*N<SPEIYIFHPEQLIT*REDAVLDHALGHSIIGKGIITQGITR<THNLSIQCTGIQGFLL

Parental  FHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHT-TLEHSDCAFMVDN
          FHSFGG.T.S.......E.LSV...KKS.L..S..P.P..S......YNSIL.T.T.T.E.SDC.F.VDN
Retrocopy FHSFGGATSSVSSLS*WEYLSVNHSKKS*LA-SVLPPPSTSVQGCVHYNSILSTVT<TMECSDCVFIVDN

Parental  EAIYDICRRNLDIERPTYTNLNRLISQIVSS-ITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAP-
          E...D.C..N.DI..PTY...N.L.SQI..S.I.AS...DGA.NVD.T.FQ..L.P.P.IHF.LA.YAP.
Retrocopy EDNFDFCHHNWDIVCPTYIDRNYLLSQINAS<ISASFCSDGAFNVDMTVFQRKLIPCPHIHFLLAIYAP<

Parental  VISAEKAYHEQLSVA-EITNACFEPANQMVKCDP
          .I.A.K.YHEQL.VA...T.ACFEPANQ.V.CDP
Retrocopy IILA*KVYHEQLRVA<KFTIACFEPANQTVNCDP

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	410.53 RPM
SRP017611_kidney	0.00 RPM	109.98 RPM
SRP017611_liver	0.00 RPM	64.75 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2819 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2819 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2819 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460, retro_dord_564, retro_dord_786,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
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,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,
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,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531,