RetrogeneDB ID: retro_rnor_2856

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:117900009..117900729(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000043411
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Actb
• Ensembl ID: ENSRNOG00000034254
• Aliases: Actb, Actx
• Description: Actin, cytoplasmic 1 Actin, cytoplasmic 1, N-terminally processed [Source:UniProtKB/Swiss-Prot;Acc:P60711]

Sequence

>retro_rnor_2856
ATGAAGGAATATATTGTTGTCCTTATTTTGAACAATAGCCCTAGCACGTGCAAAGCTGTCTTTTTGGGCGATGATGCTCC
CTAGGCCATTTTCCCCTTCAACCTGGGCCGTCCTGAGTCCCAACACATGATGGTGGGTATGGGTCAGAAGGACTCCTATG
TCAACAAGAGGGTTCAAAGAAAGAGAGGCACTCTGACTCTAAAATACCCCCACTGAACACGGCATTGCCACCTACTGGGA
CAATACGGAGAAGATCTTGCACTATAACTTCTACAACGAGCTTCGTTTGGCTCCAGAAGAGCACACTGTGCTGCTCACCA
AGGCTTCCCTGAACCTTAGGCCAACCGTAAAAAGATGACTCAGATCATGTTTGAGACCTTTAACACCCTAGCCATGTACG
TAACCATCAATTCAATGCTGTCCCTGTATGCCTCTGGTCCCACCAGTGACATTGTGATGTACTCTGGAGACAGGGTCACT
TACATTGTGCCCATCTATGAGGGCTATGCTGTCCCTGATGTCATCCTCCATTTGGACTTGACTGACTGGGACCCAACAGA
CTACCTCATGAAGATCCTGACCCAGAGTAGCTTCACACCCACAGTTGAGAGGGAAATCATGTGTAACATCAAAGAGAAGC
TGTACTGTGTTGACATAGACTCCAAGCAAGAGATGGACACTAACGCATCCTCTTCCTTCCTGAAGAAGAGCTATGAGCTG

Alignment

ORF - retro_rnor_2856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.57 %
• Parental protein coverage: 64.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          M...I..L...N....CKA.F.GDDAP.A.FP...GRP..Q..MVGMGQKDSYV....Q.KRG.LTLKYP
Retrocopy MKEYIVVLILNNSPSTCKAVFLGDDAP*AIFPFNLGRPESQHMMVGMGQKDSYVNKRVQRKRGTLTLKYP

Parental  -IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLN-PKANREKMTQIMFETFNTPAMYVAIQA
          ..EHGI.T.WD..EKI.H..FYNELR.APEEH.VLLT.A.LN.P.ANR.KMTQIMFETFNT.AMYV.I..
Retrocopy >TEHGIATYWDNTEKILHYNFYNELRLAPEEHTVLLTKASLN<P*ANRKKMTQIMFETFNTLAMYVTINS

Parental  VLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREI
          .LSLYASG.T..IVM.SGD.VT..VPIYEGYA.P..IL.LDL...D.TDYLMKILT....SFT.T.EREI
Retrocopy MLSLYASGPTSDIVMYSGDRVTYIVPIYEGYAVPDVILHLDLTDWDPTDYLMKILTQS--SFTPTVEREI

Parental  VRDIKEKLCYVALDFEQEMATAASSSSLEKSYEL
          ...IKEKL..V..D..QEM.T.ASSS.L.KSYEL
Retrocopy MCNIKEKLYCVDIDSKQEMDTNASSSFLKKSYEL

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	855.93 RPM
SRP017611_kidney	0.00 RPM	1102.49 RPM
SRP017611_liver	0.00 RPM	363.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2856 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2856 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Homo sapiens	ENSG00000075624	6 retrocopies	retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gorilla gorilla	ENSGGOG00000001133	18 retrocopies	retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Meleagris gallopavo	ENSMGAG00000003960	2 retrocopies	retro_mgal_5, retro_mgal_6,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Mustela putorius furo	ENSMPUG00000016612	2 retrocopies	retro_mputfur_440, retro_mputfur_461,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus	ENSOANG00000007716	2 retrocopies	retro_oana_4, retro_oana_8,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus	ENSRNOG00000034254	10 retrocopies	retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856 , retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sarcophilus harrisii	ENSSHAG00000012694	4 retrocopies	retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus	ENSSTOG00000014797	3 retrocopies	retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,