RetrogeneDB ID: retro_mmus_3448

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:48010021..48010466(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Calm3
• Ensembl ID: ENSMUSG00000019370
• Aliases: Calm3, CaMA, R75142
• Description: calmodulin 3 [Source:MGI Symbol;Acc:MGI:103249]

Sequence

>retro_mmus_3448
ATGGCTGACCAACTGACTGAAGAGCAGATTGCAGAGTTCAAAGACGCTTTCTCACTATTTGACAAGGACGGGGATGGGAA
AATAACAACAAAGGAGCTGGGGACAGTGATGAGGTCCCTGGGGCAGAACCCCACAGAAGCAGAGCTGCAGGACATGATCA
ATGAAGTAGATGCAGCTAGTAATGGCACAATTGATTTCCCTGAATTTATGACAATGATGGCAAGAACAATGAAAGACAGA
CAGTGAAGAAGAAATTAGAGAAGCATTCCGTGTGTTTGATAAGGATGAAAATGGCTATATTAGTGCAGCAGAGCTTCGCC
ATGTGATGACAAACCTTGGAGAGAAGTTAACAGATGAAGAGGTCGATGAGATGATCAGGGAAGCAGACATTGATGGGGAT
GGTCAGGTAAACTACGAAGAGTTTGTACAAATGATGACAGTAAAG

Alignment

ORF - retro_mmus_3448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
          MADQLTEEQIAEFK.AFSLFDKDGDG.ITTKELGTVMRSLGQNPTEAELQDMINEVDA..NGTIDFPEF.
Retrocopy MADQLTEEQIAEFKDAFSLFDKDGDGKITTKELGTVMRSLGQNPTEAELQDMINEVDAASNGTIDFPEFM

Parental  TMMARKMKD-TDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNY
          TMMAR.MKD....EE.IREAFRVFDKD.NGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNY
Retrocopy TMMARTMKD>DSEEE-IREAFRVFDKDENGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNY

Parental  EEFVQMMTAK
          EEFVQMMT.K
Retrocopy EEFVQMMTVK

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	1.68 RPM	1087.59 RPM
SRP007412_cerebellum	0.48 RPM	1092.09 RPM
SRP007412_heart	0.19 RPM	194.07 RPM
SRP007412_kidney	0.10 RPM	271.81 RPM
SRP007412_liver	0.41 RPM	56.58 RPM
SRP007412_testis	1.28 RPM	618.48 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3448 was not detected

EST

No EST(s) were mapped for retro_mmus_3448 retrocopy.

TSS

No TSS is located nearby retro_mmus_3448 retrocopy 5' end.

Lab

retro_mmus_3448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3448 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015712	1 retrocopy	retro_acar_45,
Ailuropoda melanoleuca	ENSAMEG00000008565	3 retrocopies	retro_amel_1209, retro_amel_1562, retro_amel_421,
Bos taurus	ENSBTAG00000014583	2 retrocopies	retro_btau_113, retro_btau_135,
Canis familiaris	ENSCAFG00000029151	4 retrocopies	retro_cfam_121, retro_cfam_164, retro_cfam_225, retro_cfam_68,
Cavia porcellus	ENSCPOG00000001612	1 retrocopy	retro_cpor_1316,
Erinaceus europaeus	ENSEEUG00000000140	1 retrocopy	retro_eeur_468,
Echinops telfairi	ENSETEG00000009377	5 retrocopies	retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Felis catus	ENSFCAG00000004995	1 retrocopy	retro_fcat_1726,
Homo sapiens	ENSG00000160014	3 retrocopies	retro_hsap_1255, retro_hsap_1785, retro_hsap_59,
Gorilla gorilla	ENSGGOG00000000212	4 retrocopies	retro_ggor_187, retro_ggor_2234, retro_ggor_522, retro_ggor_988,
Loxodonta africana	ENSLAFG00000001155	5 retrocopies	retro_lafr_100, retro_lafr_156, retro_lafr_631, retro_lafr_646, retro_lafr_86,
Microcebus murinus	ENSMICG00000013180	3 retrocopies	retro_mmur_1032, retro_mmur_1447, retro_mmur_501,
Myotis lucifugus	ENSMLUG00000010528	1 retrocopy	retro_mluc_2477,
Monodelphis domestica	ENSMODG00000009222	1 retrocopy	retro_mdom_1126,
Mustela putorius furo	ENSMPUG00000005261	1 retrocopy	retro_mputfur_404,
Mus musculus	ENSMUSG00000001175	4 retrocopies	retro_mmus_1519, retro_mmus_2859, retro_mmus_2871, retro_mmus_50,
Mus musculus	ENSMUSG00000019370	3 retrocopies	retro_mmus_2879, retro_mmus_3448 , retro_mmus_454,
Nomascus leucogenys	ENSNLEG00000002752	2 retrocopies	retro_nleu_1407, retro_nleu_3097,
Otolemur garnettii	ENSOGAG00000014764	2 retrocopies	retro_ogar_2085, retro_ogar_3311,
Procavia capensis	ENSPCAG00000005751	1 retrocopy	retro_pcap_7,
Petromyzon marinus	ENSPMAG00000003323	1 retrocopy	retro_pmar_12,
Pongo abelii	ENSPPYG00000010154	4 retrocopies	retro_pabe_1106, retro_pabe_1466, retro_pabe_3238, retro_pabe_3676,
Pelodiscus sinensis	ENSPSIG00000013173	1 retrocopy	retro_psin_9,
Ictidomys tridecemlineatus	ENSSTOG00000014352	1 retrocopy	retro_itri_1018,