RetrogeneDB ID: retro_rnor_2842

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:107409445..107410068(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000007501
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gstp1
• Ensembl ID: ENSRNOG00000018237
• Aliases: Gstp1, GST-P, Gst3, Gstp, Gstp2
• Description: Glutathione S-transferase P [Source:UniProtKB/Swiss-Prot;Acc:P04906]

Sequence

>retro_rnor_2842
ATGCCGCCATACACCATTGTCTACTTCCCAGTTCGAGGGCGCTGTGAGGCCATGGGCATGCTGCTGGCTGACCAGGGCCA
GAGCTAGAAAGAGGAGGTGGTACCATAGATGTCTGGCTTCAAGGCTCACTCAAGCCCACTCATCTGTATGGGCAGCTACC
CAAGTTTGAGGATGGAGACCTCACCCTTTACCAGTCTAATGCCATCTTGAGGCACCTGGGCCGCTCTTTAGGGCTTTATG
GGAAAGACCAGAGGAAGGCCGCCCTAGTGGATATCGTGAATGATGGAGTGGAGGACCTTCGCTGCAAATATGGTACCTTC
ATCTACACTAACTATGAGAATGGTAAGGATGACTATGTGAAATCCCTGCCTGGGCATCTGAAGCCTTTGAAACCCTGCTG
TCCCAGAACCAGGGAGGCAAAGCTTTCATCATGGGTGACCAGATTTCCTTTACTGATTACAACTTGCTGGACCTGCTGCT
GGTCCACCAAGTGCTGACCCTGGCTGCCTGGACAACTTCCCCTGCTCTCTGCCTATGTGGCTCACCTCAGTGCCCGCCCC
AAGATCAAGGCCTTTCTGTCCTCCCCCGACCATGTGAACCATCCCATCAACGGCAATGGTAAG

Alignment

ORF - retro_rnor_2842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPPYTIVYFPVRGRCEATRMLLADQGQSWKEEVV-TIDVWLQGSLKSTCLYGQLPKFEDGDLTLYQSNAI
          MPPYTIVYFPVRGRCEA..MLLADQGQS.KEEVV.TIDVWLQGSLK.T.LYGQLPKFEDGDLTLYQSNAI
Retrocopy MPPYTIVYFPVRGRCEAMGMLLADQGQS*KEEVV<TIDVWLQGSLKPTHLYGQLPKFEDGDLTLYQSNAI

Parental  LRHLGRSLGLYGKDQKEAALVDMVNDGVEDLRCKYGTLIYTNYENGKDDYVKALPGHLKP-FETLLSQNQ
          LRHLGRSLGLYGKDQ..AALVD.VNDGVEDLRCKYGT.IYTNYENGKDDYVK.LPGHLKP.FETLLSQNQ
Retrocopy LRHLGRSLGLYGKDQRKAALVDIVNDGVEDLRCKYGTFIYTNYENGKDDYVKSLPGHLKP<FETLLSQNQ

Parental  GGKAFIVGNQISFADYNLLDLLLVHQVLA-PGCLDNF-PLLSAYVARLSARPKIKAFLSSPDHLNRPING
          GGKAFI.G.QISF.DYNLLDLLLVHQVL..PGCLDNF.PLLSAYVA.LSARPKIKAFLSSPDH.N.PING
Retrocopy GGKAFIMGDQISFTDYNLLDLLLVHQVLT<PGCLDNF<PLLSAYVAHLSARPKIKAFLSSPDHVNHPING

Parental  NGK
          NGK
Retrocopy NGK

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	48.75 RPM
SRP017611_kidney	0.07 RPM	229.93 RPM
SRP017611_liver	0.00 RPM	12.78 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2842 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2842 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001020	3 retrocopies	retro_amel_1921, retro_amel_249, retro_amel_778,
Canis familiaris	ENSCAFG00000011349	4 retrocopies	retro_cfam_143, retro_cfam_2043, retro_cfam_46, retro_cfam_617,
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Macropus eugenii	ENSMEUG00000001519	2 retrocopies	retro_meug_1519, retro_meug_1762,
Myotis lucifugus	ENSMLUG00000011529	4 retrocopies	retro_mluc_1669, retro_mluc_1714, retro_mluc_1962, retro_mluc_629,
Mustela putorius furo	ENSMPUG00000004029	2 retrocopies	retro_mputfur_1215, retro_mputfur_1463,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Oryctolagus cuniculus	ENSOCUG00000002230	1 retrocopy	retro_ocun_391,
Pteropus vampyrus	ENSPVAG00000008586	6 retrocopies	retro_pvam_1119, retro_pvam_1463, retro_pvam_568, retro_pvam_664, retro_pvam_681, retro_pvam_718,
Rattus norvegicus	ENSRNOG00000018237	4 retrocopies	retro_rnor_2140, retro_rnor_2567, retro_rnor_2842 , retro_rnor_769,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Tursiops truncatus	ENSTTRG00000003746	1 retrocopy	retro_ttru_1416,
Vicugna pacos	ENSVPAG00000008003	1 retrocopy	retro_vpac_73,