RetrogeneDB ID: retro_mmus_1825

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:37388406..37389014(+)
• Located in intron of: ENSMUSG00000012443

Retrocopy information

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

Parental gene information

• Parental gene symbol: Morf4l1
• Ensembl ID: ENSMUSG00000062270
• Aliases: Morf4l1, MORFRG15, MRG15, TEG-189, Tex189, mKIAA4002
• Description: mortality factor 4 like 1 [Source:MGI Symbol;Acc:MGI:1096551]

Sequence

>retro_mmus_1825
ATGGCGCCCAAGCAGGACCCGAAGCCAAAATTCCAGGAGGGTGAGCGAGTGCTGTGCTTTCATGGCCTCTTTATGAAGCA
AAGTATGTAAAGTTGCCATAAAGGACAAACAAGTGAAATACTTCATCCATTACAGTGGTTGGGATAAAAATTGGGATGAA
TGGGTGCCAGAAAGCAGAGTACTCAAATACGCGGACACCAATTTGCAGAAACTGTGAGAACTTCAAAAGGCCAATCAGGA
ACAATATGCAGAGGGCAAGATGAGAGGGGCTGCTCCGGGGAAGAACAACAGAAAAATCCGGTCTGCAACAGAAAAATGTT
GAAGTGAAAACAAAAAAGAACAAGCAGAAAACACCTGGAAACGGAGATGGTGGCAGTACCAGTGAGACACCTCAGCCTCC
TAGGAAGAAGAGAGCCCGGGTAGATCCTACCGTTGAAAATGAAGAAACCTTCATGAACAGAGTTGAAGTTAAAGTGAAGA
CTCCTGAAGAGCTGAAACCCTGGCTTGTGGATGACTGGGACTTGATTACCAGGCAAAAGCAGCTTTTTTATCTGCCTGCC
AGGAAGAATGTGGATTCCATTTTGGAGGATTATGCAAATTATAAGGAA

Alignment

ORF - retro_mmus_1825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.99 %
• Parental protein coverage: 62.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAPKQD-PKPKFQEGERVLCFHGPLLYEAKCVK-VAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDT
          MAPKQD.P..K...G........PL.YEAK.VK.VAIKDKQVKYFIHYSGW.KNWDEWVPESRVLKY.DT
Retrocopy MAPKQD<PEAKIPGG*ASAVLSWPL-YEAKYVK<VAIKDKQVKYFIHYSGWDKNWDEWVPESRVLKYADT

Parental  NLQKQRELQKANQEQYAEGKMRGAAP-GKKT--SGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRK
          NLQK..ELQKANQEQYAEGKMRGAAP.G..T..SGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRK
Retrocopy NLQKL*ELQKANQEQYAEGKMRGAAP>GRTTEKSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRK

Parental  KRARVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKK
          KRARVDPTVENEETFMNRVEVKVK.PEELKPWLVDDWDLITRQKQLFYLPA.KNVDSILEDYANYK.
Retrocopy KRARVDPTVENEETFMNRVEVKVKTPEELKPWLVDDWDLITRQKQLFYLPARKNVDSILEDYANYKE

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	63.48 RPM
SRP007412_cerebellum	0.00 RPM	59.70 RPM
SRP007412_heart	0.09 RPM	56.63 RPM
SRP007412_kidney	0.04 RPM	53.38 RPM
SRP007412_liver	0.00 RPM	54.75 RPM
SRP007412_testis	0.14 RPM	301.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1825 was not detected

EST

1 EST(s) were mapped to retro_mmus_1825 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV571078	37388417	37388743	99.7	320	0	316

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_64256	755 libraries	275 libraries	42 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_1825 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_1825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1825 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012344	1 retrocopy	retro_amel_124,
Bos taurus	ENSBTAG00000010988	1 retrocopy	retro_btau_137,
Canis familiaris	ENSCAFG00000014113	1 retrocopy	retro_cfam_20,
Callithrix jacchus	ENSCJAG00000002214	5 retrocopies	retro_cjac_2113, retro_cjac_2280, retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Homo sapiens	ENSG00000185787	3 retrocopies	retro_hsap_309, retro_hsap_3125, retro_hsap_850,
Gorilla gorilla	ENSGGOG00000016826	3 retrocopies	retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana	ENSLAFG00000009851	1 retrocopy	retro_lafr_62,
Macaca mulatta	ENSMMUG00000022926	1 retrocopy	retro_mmul_1064,
Monodelphis domestica	ENSMODG00000011517	2 retrocopies	retro_mdom_150, retro_mdom_158,
Mustela putorius furo	ENSMPUG00000015429	1 retrocopy	retro_mputfur_180,
Mus musculus	ENSMUSG00000062270	9 retrocopies	retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825 , retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys	ENSNLEG00000008678	3 retrocopies	retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus	ENSOCUG00000015117	2 retrocopies	retro_ocun_108, retro_ocun_21,
Otolemur garnettii	ENSOGAG00000006047	4 retrocopies	retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii	ENSPPYG00000006703	4 retrocopies	retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes	ENSPTRG00000007351	3 retrocopies	retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus	ENSRNOG00000014410	6 retrocopies	retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sarcophilus harrisii	ENSSHAG00000018402	1 retrocopy	retro_shar_393,
Sus scrofa	ENSSSCG00000001769	1 retrocopy	retro_sscr_93,
Ictidomys tridecemlineatus	ENSSTOG00000013294	3 retrocopies	retro_itri_111, retro_itri_1545, retro_itri_1608,