RetrogeneDB ID: retro_mmus_90

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:55565291..55566386(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000063129
• Aliases: Aldoart2, 4933425L11Rik, Aldo1-ps1, Aldoa-ps1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Aldoa
• Ensembl ID: ENSMUSG00000030695
• Aliases: Aldoa, Aldo-1, Aldo1
• Description: aldolase A, fructose-bisphosphate [Source:MGI Symbol;Acc:MGI:87994]

Sequence

>retro_mmus_90
ATGTCTTACCCCTACCCAGCACTGACCCCGGAGCAGAAGAAGGAGCTGTCTGACATCGCTCGCCGAATTGTGGCTCCGGG
CAAGGGCATCCTGGCTGCAGATGAGTCCACTGGAAGCATTGCCAAGCGGCTGCAGTCCATTGGCACCGAGAACACCGAGG
AGAACAGACGCTTCTACCGTCAGCTGCTGCTGACTGCCGACGACCGTGTGAATCCCTGCATTGGGGGTGTGATCCTCTTC
CATGAGACACTGTACCAGAAGGCAGATGATGGACGTCCCTTCCCCCAGATTATCAAGTCCAAGGGTGGTGTTGTGGGCAT
TAAGGTGGACAAGGGCGTGGTGCCCCTGGCAGGAACTAACGGCGAGACCACCACCCAAGGGCTGGATGATCTGTCTGGAC
GCTGTGCTCAGTACAAGCAGGATGGGGCCGATTTTGCCAAATGGCGCTGTGTGCTGAAGATTGGGAAACACACCCCCTCA
GCCCTCGCCATTATGGAAAATGCCAATGTTCTGGCTCATTACGCCAGCATCTGCCAGCAGAATGGCATTGTACCCATTGT
GGAGCCAGAAATCCTCCCTGATGGCGACCATGACTTGAAGCACTGTCAGTATGTAACTGAGAAGGTACTGGCCGCTGTCT
ACAAGGCTCTGAGCGACCACCATGTCTACCTGGAAGGAACCTTACTGAAGCCCAACATGGTCACCGCAGGCCATGCTTGC
ACTCAGGTATTTTCCAGTGAAGAGATTGCCATGGCAACTGTCACAGCACTTCGTCGCACAGTGCCCCCTGCTGTCCCTGG
AGTCACTTTCCTGTCTGGAGGACAGAGTGAAGAAGAGGCATCCATCAACCTCAATGCTATCAACAAGTGTCCCCTGCTGA
AGCCGTGGGCCTTGACTTTCTCCTATGGCCGAGCCCTGCAGGCTTCTGCCCTAAAGGCCTGGGGTGGGAAGAAGGAGAAC
ACGAAGGATGCCCAAGAGGAGTACATCAAGCGAGCCCAGGCCAACAGCCTTGCTTGTCAAGGAAAGTACACCCCAAGCAA
TGAGTCAGGGGCAGCCGCCAGTGAATCCCTCTTCATCTCTAACCACGCCTACTGA

Alignment

ORF - retro_mmus_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPHPYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRV
          M..PYPALTPEQKKELSDIA.RIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRV
Retrocopy MSYPYPALTPEQKKELSDIARRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRV

Parental  NPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKK
          NPCIGGVILFHETLYQKADDGRPFPQ.IKSKGGVVGIKVDKGVVPLAGTNGETTTQGLD.LS.RCAQYK.
Retrocopy NPCIGGVILFHETLYQKADDGRPFPQIIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDDLSGRCAQYKQ

Parental  DGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVL
          DGADFAKWRCVLKIG.HTPSALAIMENANVLA.YASICQQNGIVPIVEPEILPDGDHDLK.CQYVTEKVL
Retrocopy DGADFAKWRCVLKIGKHTPSALAIMENANVLAHYASICQQNGIVPIVEPEILPDGDHDLKHCQYVTEKVL

Parental  AAVYKALSDHHVYLEGTLLKPNMVTPGHACTQKFSNEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEA
          AAVYKALSDHHVYLEGTLLKPNMVT.GHACTQ.FS.EEIAMATVTALRRTVPPAV.GVTFLSGGQSEEEA
Retrocopy AAVYKALSDHHVYLEGTLLKPNMVTAGHACTQVFSSEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEA

Parental  SINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYIKRALANSLACQGKYTPSGQSG
          SINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKEN.K.AQEEYIKRA.ANSLACQGKYTPS..SG
Retrocopy SINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENTKDAQEEYIKRAQANSLACQGKYTPSNESG

Parental  AAASESLFISNHAY
          AAASESLFISNHAY
Retrocopy AAASESLFISNHAY

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	0.16 RPM	1035.35 RPM
SRP007412_cerebellum	0.17 RPM	1045.41 RPM
SRP007412_heart	0.09 RPM	2044.01 RPM
SRP007412_kidney	0.13 RPM	1259.68 RPM
SRP007412_liver	0.03 RPM	87.00 RPM
SRP007412_testis	165.16 RPM	329.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_90 was not detected

EST

2 EST(s) were mapped to retro_mmus_90 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BU743808	55565224	55565819	100	595	0	595
CN838207	55565204	55565796	100	588	0	584

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_23704	1047 libraries	18 libraries	1 library	0 libraries	6 libraries
TSS #2	TSS_23705	1064 libraries	4 libraries	2 libraries	0 libraries	2 libraries

The graphical summary, for retro_mmus_90 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_90 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_90 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_226

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90 ,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,