RetrogeneDB ID: retro_mmus_920

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:13455022..13455970(-)
• Located in intron of: ENSMUSG00000020576

Retrocopy information

• Ensembl ID: ENSMUSG00000071414
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Akr1b3
• Ensembl ID: ENSMUSG00000001642
• Aliases: Akr1b3, ALR2, AR, Ahr-1, Ahr1, Akr1b1, Aldor1, Aldr1
• Description: aldo-keto reductase family 1, member B3 (aldose reductase) [Source:MGI Symbol;Acc:MGI:1353494]

Sequence

>retro_mmus_920
ATGGCCAGCCATCTGGAACTCAACAACGGCACCAAGATGCCCACCCTGGGCCTGGGCACCTGGAAGTCCCCTCCTGGCCA
GGTGACTGAGGCCGTGAAGGTTGCTATTGACTTGGGGTACCGCCACATTGACTGCGCCCAGGTGTACCAGAATGAGAAGG
AGGTGGGAGTGGCCCTCCAGGAGAAGCTCAAGGAGCAGGTGGTGAAGCGGCAGGATCTCTTCATTGTCAGCAAGCTGTGG
TGCACGTTCCATGACAAGAGCATGGTGAAAGGAGCCTTCCAGAAGACACTGAGCGACCTGCAGCTGGACTACCTGGATCT
CTACCTTATTCACTGGCCAACGGGGTTCAAGCCTGGGCCCGACTATTTCCCACTGGATGCCTCAGGGAACGTGATACCTA
GTGACACCGATTTTGTGGACACTTGGACGGCTATGGAACAACTAGTGAATGAAGGTTTGGTGAAAACAATCGGTGTCTCC
AACTTCAACCCTCTTCAGATTGAGAGGATCTTGAACAAACCTGGCTTAAAATATAAGCCTGCGGTGAACCAGATCGAGTG
CCACCCGTACCTAACTCAGGAGAAGCTGATTGAATACTGCCACAGCAAAGGCATCGTGGTGACAGCATACAGTCCCCTTG
GTTCTCCTGACAGGCCCTGGGCCAAGCCTGAAGACCCGTCTCTCCTGGAGGATCCCAGGATCAAAGCAATTGCAGCCAAG
TACAATAAAACTACAGCCCAGGTGCTGATCCGGTTCCCCATTCAGAGGAACTTGGTAGTGATCCCCAAGTCTGTGACACC
AGTGCGCATTGCTGAGAACTTGAAGGTCTTTGACTTTGAGCTGAGCAGCGAGGACATGGCCACTCTACTCAGCTACAACA
GGAACTGGAGGGTGTGCGCCTTGATGAGCTGTGCCAAACACAAGGATTACCCCTTCCACGCCGAAGTC

Alignment

ORF - retro_mmus_920 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASHLELNNGTKMPTLGLGTWKSPPGQVTEAVKVAIDLGYRHIDCAQVYQNEKEVGVALQEKLKEQVVKR
          MASHLELNNGTKMPTLGLGTWKSPPGQVTEAVKVAIDLGYRHIDCAQVYQNEKEVGVALQEKLKEQVVKR
Retrocopy MASHLELNNGTKMPTLGLGTWKSPPGQVTEAVKVAIDLGYRHIDCAQVYQNEKEVGVALQEKLKEQVVKR

Parental  QDLFIVSKLWCTFHDKSMVKGAFQKTLSDLQLDYLDLYLIHWPTGFKPGPDYFPLDASGNVIPSDTDFVD
          QDLFIVSKLWCTFHDKSMVKGAFQKTLSDLQLDYLDLYLIHWPTGFKPGPDYFPLDASGNVIPSDTDFVD
Retrocopy QDLFIVSKLWCTFHDKSMVKGAFQKTLSDLQLDYLDLYLIHWPTGFKPGPDYFPLDASGNVIPSDTDFVD

Parental  TWTAMEQLVDEGLVKTIGVSNFNPLQIERILNKPGLKYKPAVNQIECHPYLTQEKLIEYCHSKGIVVTAY
          TWTAMEQLV.EGLVKTIGVSNFNPLQIERILNKPGLKYKPAVNQIECHPYLTQEKLIEYCHSKGIVVTAY
Retrocopy TWTAMEQLVNEGLVKTIGVSNFNPLQIERILNKPGLKYKPAVNQIECHPYLTQEKLIEYCHSKGIVVTAY

Parental  SPLGSPDRPWAKPEDPSLLEDPRIKAIAAKYNKTTAQVLIRFPIQRNLVVIPKSVTPVRIAENLKVFDFE
          SPLGSPDRPWAKPEDPSLLEDPRIKAIAAKYNKTTAQVLIRFPIQRNLVVIPKSVTPVRIAENLKVFDFE
Retrocopy SPLGSPDRPWAKPEDPSLLEDPRIKAIAAKYNKTTAQVLIRFPIQRNLVVIPKSVTPVRIAENLKVFDFE

Parental  VSSEDMATLLSYNRNWRVCALMSCAKHKDYPFHAEV
          .SSEDMATLLSYNRNWRVCALMSCAKHKDYPFHAEV
Retrocopy LSSEDMATLLSYNRNWRVCALMSCAKHKDYPFHAEV

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	0.05 RPM	11.77 RPM
SRP007412_cerebellum	0.00 RPM	5.99 RPM
SRP007412_heart	0.09 RPM	59.52 RPM
SRP007412_kidney	0.02 RPM	36.13 RPM
SRP007412_liver	0.03 RPM	3.30 RPM
SRP007412_testis	0.00 RPM	33.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_920 was not detected

EST

No EST(s) were mapped for retro_mmus_920 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_22220	668 libraries	385 libraries	19 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_920 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_920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_920 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 80 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009902	3 retrocopies	retro_btau_1092, retro_btau_1642, retro_btau_821,
Canis familiaris	ENSCAFG00000001290	1 retrocopy	retro_cfam_63,
Callithrix jacchus	ENSCJAG00000012231	14 retrocopies	retro_cjac_1140, retro_cjac_1167, retro_cjac_1718, retro_cjac_1973, retro_cjac_2550, retro_cjac_3102, retro_cjac_3143, retro_cjac_3297, retro_cjac_3692, retro_cjac_3840, retro_cjac_3872, retro_cjac_3910, retro_cjac_476, retro_cjac_621,
Dasypus novemcinctus	ENSDNOG00000011358	2 retrocopies	retro_dnov_2214, retro_dnov_721,
Homo sapiens	ENSG00000085662	7 retrocopies	retro_hsap_1261, retro_hsap_1422, retro_hsap_2049, retro_hsap_2663, retro_hsap_312, retro_hsap_4745, retro_hsap_851,
Gorilla gorilla	ENSGGOG00000011731	6 retrocopies	retro_ggor_1477, retro_ggor_1859, retro_ggor_2948, retro_ggor_343, retro_ggor_695, retro_ggor_991,
Macropus eugenii	ENSMEUG00000003434	6 retrocopies	retro_meug_1455, retro_meug_1505, retro_meug_1811, retro_meug_1980, retro_meug_486, retro_meug_504,
Microcebus murinus	ENSMICG00000001921	2 retrocopies	retro_mmur_1087, retro_mmur_66,
Mus musculus	ENSMUSG00000001642	10 retrocopies	retro_mmus_1252, retro_mmus_2082, retro_mmus_2678, retro_mmus_3242, retro_mmus_3488, retro_mmus_444, retro_mmus_534, retro_mmus_764, retro_mmus_784, retro_mmus_920 ,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013037	7 retrocopies	retro_nleu_1246, retro_nleu_1533, retro_nleu_2099, retro_nleu_2569, retro_nleu_2570, retro_nleu_418, retro_nleu_419,
Otolemur garnettii	ENSOGAG00000016156	2 retrocopies	retro_ogar_1282, retro_ogar_808,
Procavia capensis	ENSPCAG00000016195	1 retrocopy	retro_pcap_428,
Pongo abelii	ENSPPYG00000018017	8 retrocopies	retro_pabe_1050, retro_pabe_1089, retro_pabe_1176, retro_pabe_1672, retro_pabe_2411, retro_pabe_3691, retro_pabe_370, retro_pabe_694,
Pan troglodytes	ENSPTRG00000019716	6 retrocopies	retro_ptro_1365, retro_ptro_1794, retro_ptro_254, retro_ptro_3040, retro_ptro_3160, retro_ptro_972,
Rattus norvegicus	ENSRNOG00000009513	1 retrocopy	retro_rnor_1438,
Tupaia belangeri	ENSTBEG00000013327	1 retrocopy	retro_tbel_3093,