RetrogeneDB ID: retro_mmus_2544

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:8913094..8913954(+)
• Located in intron of: ENSMUSG00000042476

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cnn3
• Ensembl ID: ENSMUSG00000053931
• Aliases: Cnn3, 1600014M03Rik, C85854, Calpo3
• Description: calponin 3, acidic [Source:MGI Symbol;Acc:MGI:1919244]

Sequence

>retro_mmus_2544
ATAGACATTGGCAACAACTTCCAGCTGGGGCTGAAGGACAGCATCATCCTGTGCGAACTCATAAACAAGCTACAGCCAGG
CTCTGTGAAGAAAGTCAACGAATCCTCACTAAATTGGCCGCAGTTGGAGAATATCGGCAACTTCATTAAAGCTATCCAGG
CTTACGGTATGAAGCCCCATGATATATTTGAAGCAAACGACCTCTTTGAGAATGGCAACATGATCCAGGCTACGCTGGTG
GCTCTAGCAAGTCTGGCGAAAACAGAAAGATTCCAAACAACCATTGACATTGGCGTTAAGTATGCAGAAAAACAAACAAG
ACGTTTTGATGAAGGCAAATTAAAGGCTGACCAGAGTGTAATTGGTTTACAGATGGGTACAACAAATGTGCCAGCCAGGC
GGGCATGACAGCCTATGGGACTCGGAGGCATCTTTATGGTCCCAAGATGCAGACGGAGAAACCCTTTGACCAGACCACGA
TTAGCCTGCAGATGGGCACCAACAAAGGGGCCAGCCAGGCTGGGATGTTAGCACCAGGTACCAGAAGAGACATCTATGAC
CAGAAGCTGACATTACAGCCAGTGGACAACTTGACCATTTCTCTACAGATGGGCACCAACAAAGTTGCTTCCCAGAAAGG
AATGAGTGTGTATTGGCTTGGGCGGCAAGTGTATGACCCCAAGTACTGTGCCGCACCCACAGAACCTGTCATTCACAGCG
GAAGCCAGGGCACGGGCACCAATGGGTCGGAAATCAGTGATAGCGATTATCAGGCAGAATACCCCAATGAATAGCACGGC
GAGTACCCAGACGACTACCCTCGAGGGTACCAGTATGGCGATGACCAGGGCATTGATTAT

Alignment

ORF - retro_mmus_2544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.41 %
• Parental protein coverage: 87.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGIGTNFQLGLKDGIILCELINKLQPGSVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFE
          ..IG.NFQLGLKD.IILCELINKLQPGSVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFE
Retrocopy IDIGNNFQLGLKDSIILCELINKLQPGSVKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFE

Parental  NGNMTQVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQTRRFDEGKLKAGQSVIGLQMGT-NKCASQAGMT
          NGNM...Q.TLVALA.LAKT..F.TTIDIGVKYAEKQTRRFDEGKLKA.QSVIGLQMGT.NKCASQAGMT
Retrocopy NGNM--IQATLVALASLAKTERFQTTIDIGVKYAEKQTRRFDEGKLKADQSVIGLQMGT<NKCASQAGMT

Parental  AYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTN
          AYGTRRHLY.PKMQT.KPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDN.TISLQMGTN
Retrocopy AYGTRRHLYGPKMQTEKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNLTISLQMGTN

Parental  KVASQKGMSVYGLGRQVYDPKYCAAPTEPVIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYPDDYPREY
          KVASQKGMSVY.LGRQVYDPKYCAAPTEPVIH.GSQGTGTNGSEISDSDYQAEYP.E.HGEYPDDYPR.Y
Retrocopy KVASQKGMSVYWLGRQVYDPKYCAAPTEPVIHSGSQGTGTNGSEISDSDYQAEYPNE*HGEYPDDYPRGY

Parental  QYGDDQGIDY
          QYGDDQGIDY
Retrocopy QYGDDQGIDY

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	0.19 RPM	46.98 RPM
SRP007412_cerebellum	0.04 RPM	53.36 RPM
SRP007412_heart	0.16 RPM	34.71 RPM
SRP007412_kidney	0.23 RPM	122.12 RPM
SRP007412_liver	0.46 RPM	111.83 RPM
SRP007412_testis	0.00 RPM	5.58 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2544 was not detected

EST

No EST(s) were mapped for retro_mmus_2544 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_116019	482 libraries	366 libraries	200 libraries	22 libraries	2 libraries

The graphical summary, for retro_mmus_2544 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_2544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2544 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mus musculus	ENSMUSG00000004665	2 retrocopies	retro_mmus_1824, retro_mmus_2317,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544 ,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,