RetrogeneDB ID: retro_mmus_2982

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:140890886..140892077(+)
• Located in intron of: ENSMUSG00000025487

Retrocopy information

• Ensembl ID: ENSMUSG00000083396
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dnaja1
• Ensembl ID: ENSMUSG00000028410
• Aliases: Dnaja1, Hsj2, Nedd7
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:MGI Symbol;Acc:MGI:1270129]

Sequence

>retro_mmus_2982
ATGGTGAAAGAAACCGCTTACTACGATGTTTTGGGGGTAAAACCCAATGCCACCCAGGAAGAATTGAAAAAGGAATATAG
AAAATTGGCCTTGAAGTACCACCCTGATAAGAATCCAAATGAAGGAGAAAAGTTTAAACAGATTTCTCAAGCTTATGAAG
TTCTTGCTGATTCCAAAAAAAGGGAACTATATGATAAAGGAGGGGAGCAGGCGATTAAAGAGGGCGGAGCAGGTGGTGGT
TTTGGCTCACCCATGGATATCTTTGATATGTTCTTTGGAGGAGGAGGAAGAATGCAAAGAGAAAGGAGAGGTAAAAATGT
TGTTCATCAGCTCTCAGTGACCTTAGAAGACTTATATAATGGTGCAACAAGAAAACTGGCTCTGCAAAAGAATGTGATTT
GTGACAAATGTGAAGGCCGAGGTGGTAAGAAAGGAGCAGTAGAGTGCTGTCCCAACTGCCGGGGGACAGGTATGCAGATA
AGGATTCATCAGATTGGACCAGGAATGGTTCAGCAAATTCAGTCAGTGTGCATGGAGTGCCAGGGTCATGGAGAACGCAT
CAGTCCAAAAGACAGATGTAAAAGCTGCAATGGAAGAAAAATAGTTCGAGAGAAGAAAATTTTAGAAGTTCATATTGATA
AAGGCATGAAAGATGGTCAGAAGATAACATTCCACGGTGAAGGAGACCAAGAACCAGGACTGGAGCCAGGAGATATTATC
ATTGTGTTAGATCAGAAGGACCATGCTGTTTTTACAAGGCGAGGAGAAGACCTTTTTATGTGTATGGACATACAGCTGAT
TGAAGCATTGTGCGGCTTCCAAAAGCCACTATCTACTCTTGACAACCGAACCATAGTCATCACCTCTCATCCAGGTCAGA
TTGTCAAGCATGGGGATATAAAATGTGTGCTAAATGAAGGTATGCCAATATACCGTCAGCCATATGAAAAGGGACGTCTA
ATCATTGAGTTTAAGGTAAACTTTCCTGAAAATGGCTTTCTCTCTCCTGATAAACTCTCTTTGCTGGAAAAACTCCTTCC
TGAAAGGAAGGAAGTAGAAGAGACTGATGAAATGGATCAGGTAGAACTGGTGGACTTTGATCCAAATCAGGAAAGACGGC
GTCATTATAATGGAGAAGCGTATGAGGATGATGAACATCACCCCAGAGGTGGCGTTCAGTGTCAGACCTCT

Alignment

ORF - retro_mmus_2982 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLADSKKRELYDKGGEQ
          MVKET.YYDVLGVKPNATQEELKK.YRKLALKYHPDKNPNEGEKFKQISQAYEVLADSKKRELYDKGGEQ
Retrocopy MVKETAYYDVLGVKPNATQEELKKEYRKLALKYHPDKNPNEGEKFKQISQAYEVLADSKKRELYDKGGEQ

Parental  AIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
          AIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
Retrocopy AIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR

Parental  GGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEV
          GGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEV
Retrocopy GGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEV

Parental  HIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTL
          HIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQL.EALCGFQKP.STL
Retrocopy HIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLIEALCGFQKPLSTL

Parental  DNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
          DNRTIVITSHPGQIVKHGDIKCVLNEGMPIYR.PYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
Retrocopy DNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRQPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK

Parental  EVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
          EVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
Retrocopy EVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS

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	0.40 RPM	103.33 RPM
SRP007412_cerebellum	0.69 RPM	81.46 RPM
SRP007412_heart	0.34 RPM	33.68 RPM
SRP007412_kidney	0.79 RPM	125.45 RPM
SRP007412_liver	0.38 RPM	146.46 RPM
SRP007412_testis	0.37 RPM	69.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2982 was not detected

EST

8 EST(s) were mapped to retro_mmus_2982 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA414938	140891099	140891502	99.3	399	3	395
BP766104	140891059	140891567	100	508	0	508
BQ042982	140891023	140891574	100	551	0	551
BQ264795	140891107	140891609	98.7	495	7	488
BY367714	140891081	140891474	99	389	4	385
CA555148	140891054	140891480	99.8	425	1	424
CD543486	140891048	140891566	100	518	0	518
CN714919	140891061	140891553	99.8	491	1	490

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_130459	363 libraries	469 libraries	221 libraries	16 libraries	3 libraries

The graphical summary, for retro_mmus_2982 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_2982 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2982 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Callithrix jacchus	ENSCJAG00000008022	10 retrocopies	retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus	ENSCPOG00000000462	6 retrocopies	retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus	ENSMLUG00000016086	7 retrocopies	retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mus musculus	ENSMUSG00000028410	3 retrocopies	retro_mmus_2561, retro_mmus_2982 , retro_mmus_3507,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Procavia capensis	ENSPCAG00000012273	2 retrocopies	retro_pcap_184, retro_pcap_220,
Pteropus vampyrus	ENSPVAG00000011470	1 retrocopy	retro_pvam_672,
Rattus norvegicus	ENSRNOG00000007029	2 retrocopies	retro_rnor_2208, retro_rnor_608,
Sorex araneus	ENSSARG00000001373	5 retrocopies	retro_sara_280, retro_sara_312, retro_sara_671, retro_sara_741, retro_sara_748,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Ictidomys tridecemlineatus	ENSSTOG00000005200	4 retrocopies	retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Tarsius syrichta	ENSTSYG00000001329	4 retrocopies	retro_tsyr_110, retro_tsyr_1384, retro_tsyr_1921, retro_tsyr_57,