RetrogeneDB ID: retro_mmus_696

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:19720629..19721469(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082100
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Glul
• Ensembl ID: ENSMUSG00000026473
• Aliases: Glul, GS, Glns
• Description: glutamate-ammonia ligase (glutamine synthetase) [Source:MGI Symbol;Acc:MGI:95739]

Sequence

>retro_mmus_696
AACAAGCTGGTGCTATGTGAAGTTTTCAAGTATAACCGGAAGCCTGCAGAGACCAACTTGAGGCACATCTGTAAACGGAT
AATGGACATGGTGAGCAACCAGCACCCCTGGTTTGGAATGGAGCAGGAATATACTCTCATGGGAACAGACGGCCACCCGT
TTGGTTGGCCTTTCAATGGCTTCCCTGGACCCCAAGGCCCATATTACTGCGGTGTGGGAGCAGACAAGGCCTACGGCAGG
GACATCGTGGAGGCTCACTACCGGGCCTGCTTGTATGCCGGAGTCAAGATCACGGGGACAAATGCGGAGGTTATGCCTGC
CCAGTGGGAATTCCAGATAGGACCCTGTGAGGGGATCCGAATGGGAGATCATCTTTGGATAGCCTGTTTTATCTTGCATC
GGGTATGCGAAGACTTTGGGGTGATAGCAACCTTTGACCCCAAGCCCATTCCAGGGAACTGGGATGGTGCAGGCTGCCAT
ACCAACTTCAGCACCAAGGCCATGCGGGAGGAGAATGGTCTGAAGTGCATTGAGGAGGCCATTGACAAACTGAGCAAGAG
GCACCAGTACCACATCCACACCTACGATCCCAAGGGGGGCCTGGACAACTCCCGGCGTCTGACTGGATTCCACGAAACCT
CCAACATCAACGACTTTTCTGCCAGTGTTGCCAACCGCAGTGCCAGTATCCGCATTCCCTGGACTGTCGGCCAGGAGAAG
AAGGGCTACTTTGAAGACCGTCGGCCTTCTGCCAATTGTGACCCCTATGCGGTGACAGAAGCCATCGTCCGCACGTGTCT
CCTCAACGAAACAGGCGACGAACCCTTCCAATACAAGAAC

Alignment

ORF - retro_mmus_696 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.79 %
• Parental protein coverage: 75.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKLVLCEVFKYNRKPAETNLRHICKRIMDMVSNQHPWFGMEQEYTLMGTDGHPFGWPSNGFPGPQGPYYC
          NKLVLCEVFKYNRKPAETNLRHICKRIMDMVSNQHPWFGMEQEYTLMGTDGHPFGWP.NGFPGPQGPYYC
Retrocopy NKLVLCEVFKYNRKPAETNLRHICKRIMDMVSNQHPWFGMEQEYTLMGTDGHPFGWPFNGFPGPQGPYYC

Parental  GVGADKAYGRDIVEAHYRACLYAGVKITGTNAEVMPAQWEFQIGPCEGIRMGDHLWIARFILHRVCEDFG
          GVGADKAYGRDIVEAHYRACLYAGVKITGTNAEVMPAQWEFQIGPCEGIRMGDHLWIA.FILHRVCEDFG
Retrocopy GVGADKAYGRDIVEAHYRACLYAGVKITGTNAEVMPAQWEFQIGPCEGIRMGDHLWIACFILHRVCEDFG

Parental  VIATFDPKPIPGNWNGAGCHTNFSTKAMREENGLKCIEEAIDKLSKRHQYHIRAYDPKGGLDNARRLTGF
          VIATFDPKPIPGNW.GAGCHTNFSTKAMREENGLKCIEEAIDKLSKRHQYHI..YDPKGGLDN.RRLTGF
Retrocopy VIATFDPKPIPGNWDGAGCHTNFSTKAMREENGLKCIEEAIDKLSKRHQYHIHTYDPKGGLDNSRRLTGF

Parental  HETSNINDFSAGVANRGASIRIPRTVGQEKKGYFEDRRPSANCDPYAVTEAIVRTCLLNETGDEPFQYKN
          HETSNINDFSA.VANR.ASIRIP.TVGQEKKGYFEDRRPSANCDPYAVTEAIVRTCLLNETGDEPFQYKN
Retrocopy HETSNINDFSASVANRSASIRIPWTVGQEKKGYFEDRRPSANCDPYAVTEAIVRTCLLNETGDEPFQYKN

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	1.07 RPM	1095.42 RPM
SRP007412_cerebellum	0.43 RPM	796.13 RPM
SRP007412_heart	0.22 RPM	254.02 RPM
SRP007412_kidney	0.92 RPM	881.36 RPM
SRP007412_liver	0.82 RPM	1212.55 RPM
SRP007412_testis	0.73 RPM	420.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_696 was not detected

EST

No EST(s) were mapped for retro_mmus_696 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_11337	563 libraries	405 libraries	95 libraries	4 libraries	5 libraries

The graphical summary, for retro_mmus_696 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_696 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_696 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013631	4 retrocopies	retro_btau_1050, retro_btau_1474, retro_btau_336, retro_btau_824,
Canis familiaris	ENSCAFG00000013102	2 retrocopies	retro_cfam_1691, retro_cfam_2143,
Callithrix jacchus	ENSCJAG00000004654	1 retrocopy	retro_cjac_2837,
Dasypus novemcinctus	ENSDNOG00000013948	4 retrocopies	retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus	ENSECAG00000015865	1 retrocopy	retro_ecab_979,
Echinops telfairi	ENSETEG00000008329	3 retrocopies	retro_etel_143, retro_etel_189, retro_etel_1968,
Felis catus	ENSFCAG00000010551	1 retrocopy	retro_fcat_1811,
Homo sapiens	ENSG00000135821	4 retrocopies	retro_hsap_2364, retro_hsap_3255, retro_hsap_848, retro_hsap_935,
Gorilla gorilla	ENSGGOG00000024712	3 retrocopies	retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana	ENSLAFG00000000700	1 retrocopy	retro_lafr_196,
Macropus eugenii	ENSMEUG00000001774	6 retrocopies	retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta	ENSMMUG00000022884	2 retrocopies	retro_mmul_2047, retro_mmul_954,
Monodelphis domestica	ENSMODG00000006787	4 retrocopies	retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus	ENSMUSG00000026473	3 retrocopies	retro_mmus_1730, retro_mmus_1767, retro_mmus_696 ,
Nomascus leucogenys	ENSNLEG00000018007	3 retrocopies	retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii	ENSPPYG00000000440	1 retrocopy	retro_pabe_2698,
Pan troglodytes	ENSPTRG00000001751	4 retrocopies	retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii	ENSSHAG00000000116	1 retrocopy	retro_shar_553,
Sus scrofa	ENSSSCG00000015545	1 retrocopy	retro_sscr_726,
Ictidomys tridecemlineatus	ENSSTOG00000014529	2 retrocopies	retro_itri_1083, retro_itri_743,
Tupaia belangeri	ENSTBEG00000003522	3 retrocopies	retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta	ENSTSYG00000002066	1 retrocopy	retro_tsyr_385,
Tursiops truncatus	ENSTTRG00000010781	1 retrocopy	retro_ttru_543,
Drosophila melanogaster	FBgn0001145	1 retrocopy	retro_dmel_44,