RetrogeneDB ID: retro_mmus_521

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:192073822..192074452(-)
• Located in intron of: ENSMUSG00000026637

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gstp2
• Ensembl ID: ENSMUSG00000038155
• Aliases: Gstp2, GSTpiA, Gst-3, Gst3
• Description: glutathione S-transferase, pi 2 [Source:MGI Symbol;Acc:MGI:95864]

Sequence

>retro_mmus_521
ATGCCGCCGTACACCATTGTCTACTTCCCAAGTCGAGGGCGGTGTGAGGCCATGCGCATGCTGCTGACTGACCAGGGCCA
GAGCTGGAAGGAGGAGGTGGTTACCATAGATACCTGGATGCAAGGCTTGCTCAAGCCCACTTGTCTGTATGGGCAGCTTC
CTAAGTTTGAGGATGGAGACCTCACCCTTTACCAATCTAATGCCATCTTGAGACACCTTGGCCGCTCTTTGGGGCTTTAT
GGGAAAAACCAGAGGGAGGCCGCCCAGGTGGATATGGTGAATGATGGGGTAGAGGACCTTCGCGGCAAATATGGCACCAT
GATCTACAGAAACTATGAGAATGGTAAGAATGACTACGTGAAGGCCCTGCCTGGGCATCTGAAGCCTTTTGAGACCCTGC
TGTCCCAGAACCAGGGAGGCAAAGCTTTCATCGTGGGTGACCAGATCTCCTTTGCCGATTACAACTTGCTGGACCTGCTG
CTGATCCACCAAGTCCTGGCCCCTGGCTGCCTGGACAACTTCCCCCTGCTCTCTGCCTATGTGGCTCGCCTCAGTGCCCG
GCCCAAGATCAAGGCCTTTCTGTCCTCCCCGGAACATGTGAACCGTCCCATCAATGGCAATGGCAAACAG

Alignment

ORF - retro_mmus_521 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPYTIVYFPSPGRCEAMRMLLADQGQSWKEEVVTIDTWMQGLLKPTCLYGQLPKFEDGDLTLYQSNAIL
          MPPYTIVYFPS.GRCEAMRMLL.DQGQSWKEEVVTIDTWMQGLLKPTCLYGQLPKFEDGDLTLYQSNAIL
Retrocopy MPPYTIVYFPSRGRCEAMRMLLTDQGQSWKEEVVTIDTWMQGLLKPTCLYGQLPKFEDGDLTLYQSNAIL

Parental  RHLGRSLGLYGKNQREAAQVDMVNDGVEDLRGKYGTMIYRNYENGKNDYVKALPGHLKPFETLLSQNQGG
          RHLGRSLGLYGKNQREAAQVDMVNDGVEDLRGKYGTMIYRNYENGKNDYVKALPGHLKPFETLLSQNQGG
Retrocopy RHLGRSLGLYGKNQREAAQVDMVNDGVEDLRGKYGTMIYRNYENGKNDYVKALPGHLKPFETLLSQNQGG

Parental  KAFIVGDQISFADYNLLDLLLIHQVLAPGCLDNFPLLSAYVARLSARPKIKAFLSSPEHVNRPINGNGKQ
          KAFIVGDQISFADYNLLDLLLIHQVLAPGCLDNFPLLSAYVARLSARPKIKAFLSSPEHVNRPINGNGKQ
Retrocopy KAFIVGDQISFADYNLLDLLLIHQVLAPGCLDNFPLLSAYVARLSARPKIKAFLSSPEHVNRPINGNGKQ

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
SRP007412_brain	0.37 RPM	0.09 RPM
SRP007412_cerebellum	0.26 RPM	0.04 RPM
SRP007412_heart	0.47 RPM	2.77 RPM
SRP007412_kidney	1.17 RPM	1.17 RPM
SRP007412_liver	2.81 RPM	2.13 RPM
SRP007412_testis	0.18 RPM	0.18 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_521 was not detected

EST

No EST(s) were mapped for retro_mmus_521 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_73456	484 libraries	435 libraries	127 libraries	11 libraries	15 libraries
TSS #2	TSS_73457	870 libraries	152 libraries	49 libraries	0 libraries	1 library
TSS #3	TSS_73458	912 libraries	119 libraries	40 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_521 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_521 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_521 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 34 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	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521 ,
Mus musculus	ENSMUSG00000058135	1 retrocopy	retro_mmus_2692,
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,
Tursiops truncatus	ENSTTRG00000003746	1 retrocopy	retro_ttru_1416,
Vicugna pacos	ENSVPAG00000008003	1 retrocopy	retro_vpac_73,