RetrogeneDB ID: retro_rnor_1024

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:97413396..97413889(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Glo1
• Ensembl ID: ENSRNOG00000000541
• Aliases: None
• Description: Lactoylglutathione lyase [Source:UniProtKB/Swiss-Prot;Acc:Q6P7Q4]

Sequence

>retro_rnor_1024
GAGCCACAACTCTCATCCAGCAGTCTCACAGATGAGGAGACCCTCAGCTGCTGCTCTGATTGAGTCTCCAACACCAAGCA
TTTTCTACTGCAACAAACGATGCTAAGAGTTAGTGATCCGGAGTCCCTGAGTTTTCATAGGAGGATTCTGGGACTGACTT
GACTCCAGAAGTTTGATTTTCCTACTATGAAGTTTTCACTCTTATTTCTTAGTTTATCAATGTAAGAATGACATCCCCAA
AGATAAGAATGAAAGGATAGCAAAGATATTCTACAGAAAAGCCACACTTGAGTTGACACACAACTGGAGATCTGAAGATG
ACGAGACTCAGAGTTACCACAGTGGCTACTCAGACCCTCAGGGGTTTGGTCACATTAGGATTGCTGTTCATGATGCCAAT
GGTGCATGTAAGATATATGAAGAACTGGTAGTCACATGTATGAAGAAACCCAAGGATGGTAAAATGAAAGGTCTGGCATT
TGTTCAAGATCCT

Alignment

ORF - retro_rnor_1024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.69 %
• Parental protein coverage: 89.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPQPASSGLTDEAALSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPSMKFSL-Y
          EPQ..SS.LTDE..LSCCSD....TK.FLLQQTMLR..DP..SL.F..R.LGLT.LQK.DFP.MKFSL.Y
Retrocopy EPQLSSSSLTDEETLSCCSD*VSNTKHFLLQQTMLRVSDPE-SLSFHRRILGLT*LQKFDFPTMKFSL>Y

Parental  FLAYEDKNDIPKDKTERTAWAFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYEACKR
          FL.Y..KNDIPKDK.ER.A..F.RKATLELTHNW..EDDETQSYH.G.SDP.GFGHI.IAV.D...ACK.
Retrocopy FLVYQCKNDIPKDKNERIAKIFYRKATLELTHNWRSEDDETQSYHSGYSDPQGFGHIRIAVHDANGACKI

Parental  FEELGVKFVKKPDDGKMKGLAFVQDP
          .EEL.V...KKP.DGKMKGLAFVQDP
Retrocopy YEELVVTCMKKPKDGKMKGLAFVQDP

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	67.80 RPM
SRP017611_kidney	0.00 RPM	58.83 RPM
SRP017611_liver	0.00 RPM	47.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1024 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1024 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	ENSBTAG00000012703	2 retrocopies	retro_btau_1003, retro_btau_1513,
Cavia porcellus	ENSCPOG00000010050	1 retrocopy	retro_cpor_1482,
Dasypus novemcinctus	ENSDNOG00000019598	6 retrocopies	retro_dnov_1016, retro_dnov_1064, retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
Dipodomys ordii	ENSDORG00000006369	1 retrocopy	retro_dord_21,
Macropus eugenii	ENSMEUG00000005978	1 retrocopy	retro_meug_1641,
Mus musculus	ENSMUSG00000024026	1 retrocopy	retro_mmus_1902,
Otolemur garnettii	ENSOGAG00000007945	2 retrocopies	retro_ogar_2541, retro_ogar_681,
Rattus norvegicus	ENSRNOG00000000541	2 retrocopies	retro_rnor_1012, retro_rnor_1024 ,
Sus scrofa	ENSSSCG00000027778	1 retrocopy	retro_sscr_853,
Ictidomys tridecemlineatus	ENSSTOG00000005821	1 retrocopy	retro_itri_1626,
Tupaia belangeri	ENSTBEG00000014386	1 retrocopy	retro_tbel_4376,
Tursiops truncatus	ENSTTRG00000004664	1 retrocopy	retro_ttru_90,