RetrogeneDB ID: retro_rnor_2461

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:63955808..63956631(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ghitm
• Ensembl ID: ENSRNOG00000013961
• Aliases: Ghitm, MICS1
• Description: Growth hormone-inducible transmembrane protein [Source:UniProtKB/Swiss-Prot;Acc:Q5XIA8]

Sequence

>retro_rnor_2461
ATGTTAGCTGCAAGGCTTGTGTGTCTCCAGACACTACCTTCCAGGGATAGTTTTTCGCCCGCTTTCATCACCAAGGCCTC
TCCACTTGGGAAGAATCCCTTCACAAAGAACCAATGGCTCTTAACACCCAGCAGGGAATACGCCACCAAGACAAGAATTA
GGATTCACCATGGGAAAACTGCCCAAGAACTGAAAGAGGCAGCCTTGGAACCATCAATGGGGGAAAAAAACAAACTCTTT
AAAATTGATCAGATCTCCAGGACGGTGGTTTGTTGCTGGAGGAGCAGGCATTGGTCTTGGAGCACTGTGCTACTATGGCT
TGGGAATCTCTAATGAGATCAGAGCTATGGAAAAGGCTGTACTTTGGCCTCAGTATGTAAAGGATAGAATTCATTCTACT
TACATGGACTTAGCAGGAAGTATTGGTTTAACAGCTTTGTCTGCCTTGGCACTAGTAGCCAGAACACTTGCTTTCATGAA
TTTCATGATGACAGGCTCTTGGGTGACAATTGGTGCAAGCTTTGCAGCCATGACTGGAGCTGGAATGCTAGTCCAGGCAA
TATCATGTGAGCAGAGGCCAGGCCCAAAGCATCTGGCTTGGATGCTGCATTCTGGTGTGATGGGTGCAGTCATGGCTTCT
CCTCTGACGATCTTAAGGGGCCCTCTTCTCCTGAGAGCCCAATAATATACCACTGGTATTGTGGGAGGCCTCTCTCCTGC
AGCCATGTGTGCATCTATTGAGACGTTTCTGGATGTGGAAACACCCTTGTGAGTGGGCCTGAGCCTTGTCTTTGCATCTT
CACTGGGGTCTATGTTTCTTCCC

Alignment

ORF - retro_rnor_2461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.18 %
• Parental protein coverage: 77.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLAARLVCLRTLPSR-VFQPTFITKASPLVKNSITKNQWLLTPSREYATKTRIRTHRGKTGQELKEAALE
          MLAARLVCL.TLPSR..F.P.FITKASPL.KN..TKNQWLLTPSREYATKTRIR.H.GKT.QELKEAALE
Retrocopy MLAARLVCLQTLPSRDSFSPAFITKASPLGKNPFTKNQWLLTPSREYATKTRIRIHHGKTAQELKEAALE

Parental  PSL---EKVFKIDQMGKWFV-AGGAA-VGLGALCYYGLGMSNEIGAIEKAVIWPQYVKDRIHSTYMYLAG
          PS.....K.FKIDQ.....V...G.A..GLGALCYYGLG.SNEI.A.EKAV.WPQYVKDRIHSTYM.LAG
Retrocopy PSMGEKNKLFKIDQISRTVV>VAGGAGIGLGALCYYGLGISNEIRAMEKAVLWPQYVKDRIHSTYMDLAG

Parental  SIGLTALSALAL-ARSPALMNFMMTGSWMTIGATFAAMIGAGMLVQSISYEQSPGPKHLAWMLHSGVMGA
          SIGLTALSALAL.AR..A.MNFMMTGSW.TIGA.FAAM.GAGMLVQ.IS.EQ.PGPKHLAWMLHSGVMGA
Retrocopy SIGLTALSALALVARTLAFMNFMMTGSWVTIGASFAAMTGAGMLVQAISCEQRPGPKHLAWMLHSGVMGA

Parental  VVA-PLTILGGPLLLRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLGLVFASSLGSMFLP
          V.A.PLTIL.GPLLLRA..YT.GIVGGLS..AMCA..E.FL....PL.VGL.LVFASSLGSMFLP
Retrocopy VMASPLTILRGPLLLRAQ*YTTGIVGGLSPAAMCASIETFLDVETPL*VGLSLVFASSLGSMFLP

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	165.65 RPM
SRP017611_kidney	0.00 RPM	225.89 RPM
SRP017611_liver	0.00 RPM	148.53 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2461 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2461 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461 ,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,