RetrogeneDB ID: retro_mmus_2317

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:159891470..159892240(-)
• Located in intron of: ENSMUSG00000028173

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cnn2
• Ensembl ID: ENSMUSG00000004665
• Aliases: None
• Description: calponin 2 [Source:MGI Symbol;Acc:MGI:105093]

Sequence

>retro_mmus_2317
GACTTGCAGAAGGGTCTGAAAGATGGGGTTATCCTATACACACTCATGAGCAAGCTACAGCTGGGCTTCATTCCCAAAAT
CAATCACTCTATGCAGAACTGGCACCAGCTAGAAAATCTCTCCAACTTCATCAAGGCCATGGTCAGCTATGGCATGAACC
CTGTGGACCTGTTTGAAGCCAATGACCTGTTTGAGAGCGGGAATATGACACAGGTGCAAGTGTCTCTGCTTGCAATGACT
GGAAAGGCCAAGACCAAGGGGCTGCAAAGTGAGGTGGACATTGGGGTTAAATATTCGGAGAAAAAGGAGAGGAACTTTGA
CGATGCCACCATGAAGGCCGGACAGTGCATCATCGGGCTGCAGATGGGCACCAAAAATGTGCCAGCCAGTCTGGCATGAC
AACCTGCGGTACCAGGAGACATCTATATGACCCCAAGAACCACGTCCTGCCTCCCATGGACTTCTGCACCATCAGCCTCC
AGATGGGCACCAACAAGTGTGCTAGCCAGGTGGGCATGACAACTCCAGGGACCCGGAGGCACATCTATGACACCAAGCTG
GGCACTGACAAGTGCGACAACTCTTCCATGTCCCTGTAGATGGGCTACATGCCGGGTGCCAACCAGAGCGACCAGGTCTT
CGGACTGGGGAGGCAGATCTACAACCCCAAGTATTGTCCACAGGGCTCTGTAGCTGATGGGGCTCCTGCTGGTGACAGCC
AAGACAAGGCCCCTGAATACCTGGCCTACTGCCAGGAGGAAGCCGGCTAC

Alignment

ORF - retro_mmus_2317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.15 %
• Parental protein coverage: 84.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFQKGLKDGVILCTLMNKLQPGSVPKINRSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMT
          D.QKGLKDGVIL.TLM.KLQ.G..PKIN.SMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMT
Retrocopy DLQKGLKDGVILYTLMSKLQLGFIPKINHSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMT

Parental  QVQVSLLALAGKAKTKGLQSGVDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTN-KCASQSGMTAYGTR
          QVQVSLLA..GKAKTKGLQS.VDIGVKYSEK.ERNFDDATMKAGQC.IGLQMGT..KCASQSGMT..GTR
Retrocopy QVQVSLLAMTGKAKTKGLQSEVDIGVKYSEKKERNFDDATMKAGQCIIGLQMGTK<KCASQSGMTTCGTR

Parental  RHLYDPKNHILPPMDHCTISLQMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQ
          RHLYDPKNH.LPPMD.CTISLQMGTNKCASQVGMT.PGTRRHIYDTKLGTDKCDNSSMSL.MGY..GANQ
Retrocopy RHLYDPKNHVLPPMDFCTISLQMGTNKCASQVGMTTPGTRRHIYDTKLGTDKCDNSSMSL*MGYMPGANQ

Parental  SGQVFGLGRQIYDPKYCPQGSAADGAPAGDGQGEAPEYLAYCQEEAGY
          S.QVFGLGRQIY.PKYCPQGS.ADGAPAGD.Q..APEYLAYCQEEAGY
Retrocopy SDQVFGLGRQIYNPKYCPQGSVADGAPAGDSQDKAPEYLAYCQEEAGY

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	0.00 RPM	5.35 RPM
SRP007412_cerebellum	0.00 RPM	7.43 RPM
SRP007412_heart	0.00 RPM	43.80 RPM
SRP007412_kidney	0.00 RPM	40.48 RPM
SRP007412_liver	0.03 RPM	6.55 RPM
SRP007412_testis	0.00 RPM	3.84 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2317 was not detected

EST

No EST(s) were mapped for retro_mmus_2317 retrocopy.

TSS

No TSS is located nearby retro_mmus_2317 retrocopy 5' end.

Lab

retro_mmus_2317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2317 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000064666	16 retrocopies	retro_hsap_1168, retro_hsap_1575, retro_hsap_1697, retro_hsap_2127, retro_hsap_2495, retro_hsap_255, retro_hsap_2576, retro_hsap_2764, retro_hsap_3505, retro_hsap_4168, retro_hsap_4170, retro_hsap_4175, retro_hsap_4257, retro_hsap_4269, retro_hsap_4326, retro_hsap_943,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Mus musculus	ENSMUSG00000004665	2 retrocopies	retro_mmus_1824, retro_mmus_2317 ,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,