RetrogeneDB ID: retro_mmus_2085

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:122214622..122215354(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000079966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dppa4
• Ensembl ID: ENSMUSG00000058550
• Aliases: Dppa4, 2410091M23Rik, C76608, ECAT15-1
• Description: developmental pluripotency associated 4 [Source:MGI Symbol;Acc:MGI:2157525]

Sequence

>retro_mmus_2085
ATGGAGACTGCTGGAGACAAGAAGTGGAGCACAGAAGAGCCGAAGGAAAAAGTGGAATTGCAGATGTCTAGTCAACCAAG
CACGGCTCCTGCAAAGGCTAAAGCAACGGGAAAAAAACAAAAGAAGTCGGAGACAAATAATGGTTGTAAACCAAAGGAGG
GAAAACCACAAGACATTGAGACGCCAGGACAGACTCGTAGGAAGCTGGAGTTGAGGAACGTCCCTGACTCGGCCAAAGAC
GCCAGGTTGAAGACAGCTCACAAAAAAATGAAGACTGAACCGGGGGAGGAGTCTGAGGTGACAGTTCCTCTGGAAATGGT
TCCTGTGCCAGAGGAGCAGATACCTGCCCTCATTGACCCTCCTATGCTCTATGAGGAAGTCAGCACCACCGTAGTGACTA
CACCTGCCACTGAGGCCGTGTTAGCATCTTGGGCCAGAATTGCATCCAATGCTAAGAAGTACGAGGCAGTGCCAGCCGAT
GCTTCGTCCTCATCAGAAGTCAAAGGGGAAATGTGGTGTGTGGTTCATGGGACCAGCCTTCCTGGGAACTCGCGTGGTTG
GGTTCGGCTGCAGTTCCACGCTGGACAAGCCTGGGTACCCGATAAGAAAGGAAAAGCCATTGCCCTCTTCCTGCTTCCAG
CCTGCACATTTCCACCCCCACACCTGGAGGACAACATGCTGTGCCCCAAGTGTGTTCATAAGAACAAGATCTTGACTAAG
AGCCTCGAAGGA

Alignment

ORF - retro_mmus_2085 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METAGDKKWSAEEPKEEVELQMSSQPSTAPAKAKATGKKQKKSETDNGCKPKEGKPQDTETPGQTRRKLE
          METAGDKKWS.EEPKE.VELQMSSQPSTAPAKAKATGKKQKKSET.NGCKPKEGKPQD.ETPGQTRRKLE
Retrocopy METAGDKKWSTEEPKEKVELQMSSQPSTAPAKAKATGKKQKKSETNNGCKPKEGKPQDIETPGQTRRKLE

Parental  LRNVPDSAKDARLKTAHKKMKTEPGEESEVTVPLEMVPVPEEQIPALIDPPMLYEEVSTTVVTTPATEAV
          LRNVPDSAKDARLKTAHKKMKTEPGEESEVTVPLEMVPVPEEQIPALIDPPMLYEEVSTTVVTTPATEAV
Retrocopy LRNVPDSAKDARLKTAHKKMKTEPGEESEVTVPLEMVPVPEEQIPALIDPPMLYEEVSTTVVTTPATEAV

Parental  LASWARIASNAKKYEAVPADASSSSEVKGEMWCVVHGTSLPGNSRGWVRLQFHAGQAWVPDKKGKAIALF
          LASWARIASNAKKYEAVPADASSSSEVKGEMWCVVHGTSLPGNSRGWVRLQFHAGQAWVPDKKGKAIALF
Retrocopy LASWARIASNAKKYEAVPADASSSSEVKGEMWCVVHGTSLPGNSRGWVRLQFHAGQAWVPDKKGKAIALF

Parental  LLPACTFPPPHLEDNMLCPKCVHKNKILTKSLEG
          LLPACTFPPPHLEDNMLCPKCVHKNKILTKSLEG
Retrocopy LLPACTFPPPHLEDNMLCPKCVHKNKILTKSLEG

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.04 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.14 RPM	1.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2085 was not detected

EST

No EST(s) were mapped for retro_mmus_2085 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_79579	1014 libraries	26 libraries	29 libraries	3 libraries	0 libraries

The graphical summary, for retro_mmus_2085 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_2085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010335	5 retrocopies	retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus	ENSCJAG00000020171	2 retrocopies	retro_cjac_1334, retro_cjac_1491,
Echinops telfairi	ENSETEG00000002722	1 retrocopy	retro_etel_312,
Homo sapiens	ENSG00000121570	1 retrocopy	retro_hsap_893,
Gorilla gorilla	ENSGGOG00000015121	2 retrocopies	retro_ggor_1970, retro_ggor_723,
Loxodonta africana	ENSLAFG00000016804	1 retrocopy	retro_lafr_456,
Myotis lucifugus	ENSMLUG00000016423	1 retrocopy	retro_mluc_973,
Macaca mulatta	ENSMMUG00000016901	1 retrocopy	retro_mmul_1515,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mustela putorius furo	ENSMPUG00000010206	1 retrocopy	retro_mputfur_800,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085 , retro_mmus_3656,
Mus musculus	ENSMUSG00000072419	7 retrocopies	retro_mmus_1303, retro_mmus_1832, retro_mmus_1847, retro_mmus_2391, retro_mmus_2935, retro_mmus_3699, retro_mmus_394,
Nomascus leucogenys	ENSNLEG00000004030	3 retrocopies	retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus	ENSOCUG00000016435	1 retrocopy	retro_ocun_114,
Pongo abelii	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus	ENSPVAG00000010677	1 retrocopy	retro_pvam_1237,
Rattus norvegicus	ENSRNOG00000025404	4 retrocopies	retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tursiops truncatus	ENSTTRG00000009508	1 retrocopy	retro_ttru_1772,