RetrogeneDB ID: retro_mmus_1824

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:34623681..34624604(+)
• Located in intron of: ENSMUSG00000067297

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_1824
ATGAGCTCCACTCAGTTCAAAAAAGGCCCATCCTACAGGCTCTCGGCCAAGGTCAAGAACCGATTCCTGTCCAAATATGA
CCCCCAGAAGGAAACCGAACTCTGAAACTGGATAGAGGGACTCATTGGCCTCTCTATTGGCCCTGACTTCCAGAAGGGTC
TGAAAGATGAGGTTATCTTATGCACACTCATGAACAAGCTGCAGCCTGGCTCTGTCCCCAAAATCAACTTCTCTATGCAG
AGCTAGCACCAGCTGGAAAACCTCTCGAACTTCATCAAGGCCATGGTCAGCTACAGCATGAACCCCGTGGACCTCTTTGA
AGCCAGTGACCTGTTTGAGAGCGGAAATATGGCACAGGTTCATGTGTCTCTGCTTGCCCTGGTGGGAAAGGCCAAGACCA
AGACCAAGGGGCTGCTGAGTGGTGTGAACATCATGGTCAAATATTCAGAGAAACAGTAGAGAAACTTTGACGATGCCACC
ATGAAGGCCGACCAATGCGTCATCGGGCTGCAGATGGGCACCAACAAATGTGCCAGTTAGTCTGGCATGACAGTCTATGG
TACCAGGAGACATCTCTATGACCCCAAGAACCGCATCCTGCCTCTCATGGACCACTGAACCATCAGCCTCCAGATGGGCA
CCAATAAGTGTGCCAGCCAGGTGGGCATGACCGCTCCAGGGACCTGGAGATACATCTATGACACCAAGCTGGACACCGAC
AAGTGCGACAACTCTTCCATGCCCCTGCAAATGGACTACATGCTGGGCGCCAACCAGAGCGGCCAGATCTTCGGACTGGG
GCAGCAGGTATACAACCCCAAGTATTGCCCACAGGGCTCTGCAGCTGACGGGGCTCCTGACGGGGATGAGGGCCAAGGCG
AGGTCCCTGAGTACCTGGCCATTGCCAGGAGGAAGCCAGTTAC

Alignment

ORF - retro_mmus_1824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSTQFNKGPSYGLSAEVKNRLLSKYDPQKEAELRSWIEGLTGLSIGPDFQKGLKDGVILCTLMNKLQPG
          MSSTQF.KGPSY.LSA.VKNR.LSKYDPQKE.EL..WIEGL.GLSIGPDFQKGLKD.VILCTLMNKLQPG
Retrocopy MSSTQFKKGPSYRLSAKVKNRFLSKYDPQKETEL*NWIEGLIGLSIGPDFQKGLKDEVILCTLMNKLQPG

Parental  SVPKINRSMQNWHQLENLSNFIKAMVSYGMNPVDLFEANDLFESGNMTQVQVSLLALAGKAKTK--GLQS
          SVPKIN.SMQ..HQLENLSNFIKAMVSY.MNPVDLFEA.DLFESGNM.QV.VSLLAL.GKAKTK..GL.S
Retrocopy SVPKINFSMQS*HQLENLSNFIKAMVSYSMNPVDLFEASDLFESGNMAQVHVSLLALVGKAKTKTKGLLS

Parental  GVDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILPPMDHCTISL
          GV.I.VKYSEKQ.RNFDDATMKA.QCVIGLQMGTNKCAS.SGMT.YGTRRHLYDPKN.ILP.MDH.TISL
Retrocopy GVNIMVKYSEKQ*RNFDDATMKADQCVIGLQMGTNKCAS*SGMTVYGTRRHLYDPKNRILPLMDH*TISL

Parental  QMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIYDPKYCPQGS
          QMGTNKCASQVGMTAPGT.R.IYDTKL.TDKCDNSSM.LQM.Y..GANQSGQ.FGLG.Q.Y.PKYCPQGS
Retrocopy QMGTNKCASQVGMTAPGTWRYIYDTKLDTDKCDNSSMPLQMDYMLGANQSGQIFGLGQQVYNPKYCPQGS

Parental  AADGAPAGD-GQGEAPEYLA-YCQEEAGY
          AADGAP.GD.GQGE.PEYLA..CQEEA.Y
Retrocopy AADGAPDGDEGQGEVPEYLA<HCQEEASY

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	0.02 RPM	5.35 RPM
SRP007412_cerebellum	0.00 RPM	7.43 RPM
SRP007412_heart	0.00 RPM	43.80 RPM
SRP007412_kidney	0.04 RPM	40.48 RPM
SRP007412_liver	0.00 RPM	6.55 RPM
SRP007412_testis	0.00 RPM	3.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1824 was not detected

EST

No EST(s) were mapped for retro_mmus_1824 retrocopy.

TSS

No TSS is located nearby retro_mmus_1824 retrocopy 5' end.

Lab

retro_mmus_1824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1824 has 0 orthologous retrocopies within eutheria group .

---

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,