RetrogeneDB ID: retro_mmus_1907

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:39153963..39154686(+)
• Located in intron of: ENSMUSG00000035236

Retrocopy information

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

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_1907
CTGGAGACTGCTGGGAGCAAGAAGGGAGCGCAGAAGAACAGAGGGAAGAAGTGGGATACAGATGTCAAGTCAACCAAGCA
CATCTTCTGCCAACACTAAAGCAACGGGGAAAAACAAAAAAAGTCCAAGGAAGATAACGGTTGTAAACCAAAGGAGAAAA
AAAGCACAAGATACTGAGACGCCAGGGCACACTCGCAGGAAGCCTGAGTTGAAGAATGTTACTGACTCAGCCAAAGAGGC
CAGGCTGAAGATATCTCACAAAAAAATGAAGACTGAACTGAGGGAAGAGTCTCAGGTAACAGTTGCCCTGGAAATCGTCA
CTGTACCAGAGTTGCAGATATTGCTCTCACTGATCCTTTCCTGCTCTATGAGGAAGTTAGCACCACCACTGTGACATCTG
CCTCTGAGGCAGTGCTGACTTTTTGGGCCAGAATTGCAGCCAATGCTAAGAAGTCTGAGACAGTGCTGTCCAATGCAACA
ATGAAGACCTACGGGGAAATATGGTGTGTGGTTCATGGGACAAGCCTTCCTGGGAACTCAAGTGGTCGGGTTCGGCTGCA
GTTCCATGCTGGACAAGCCTGGGTACCTGAGAAGAAAGGGAAAGCGACTGCCCTCTTTCCTGCTTTCAGCCTGCACATTT
TCACCCCCACACCTGGAGGACACAACATGTTGTGCCCCAAGTGTGTTCATTAGAACAAGGTTTTAACTAAGAGCCTTGAA
GGA

Alignment

ORF - retro_mmus_1907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.2 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  METAGDKKW-SAEEPKEEVE-LQMSSQPSTAPAKAKATGKKQKK-SETDNGCKPKEGKP-QDTETPGQTR
          .ETAG.KK..SAEE..EEV...QMSSQPST..A..KATG......S..DNGCKPKE.K..QDTETPG.TR
Retrocopy LETAGSKKG<SAEEQREEVG<IQMSSQPSTSSANTKATGXXXXX<SKEDNGCKPKEKKS>QDTETPGHTR

Parental  RKLELRNVPDSAKDARLKTAHKKMKTEPGEESEVTVPLEMVPVPEEQIP-ALIDPPMLYEEVSTTVVTTP
          RK.EL.NV.DSAK.ARLK..HKKMKTE..EES.VTV.LE.V.VPE.QI..AL.DP..LYEEVSTT.VT..
Retrocopy RKPELKNVTDSAKEARLKISHKKMKTELREESQVTVALEIVTVPELQIL<ALTDPFLLYEEVSTTTVTS-

Parental  ATEAVLASWARIASNAKKYEAVPADASSSSEVKGEMWCVVHGTSLPGNSRGWVRLQFHAGQAWVPDKKGK
          A.EAVL..WARIA.NAKK.E.V...A.......GE.WCVVHGTSLPGNS.G.VRLQFHAGQAWVP.KKGK
Retrocopy ASEAVLTFWARIAANAKKSETVLSNATMKTY--GEIWCVVHGTSLPGNSSGRVRLQFHAGQAWVPEKKGK

Parental  AIALF-LLPACTFPPPHLEDNMLCPKCVHKNKILTKSLEG
          A.ALF.......F.P.....NMLCPKCVH.NK.LTKSLEG
Retrocopy ATALFPAFSLHIFTPTPGGHNMLCPKCVH*NKVLTKSLEG

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	0.05 RPM	0.00 RPM
SRP007412_cerebellum	0.04 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	0.09 RPM	1.28 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1907 was not detected

EST

No EST(s) were mapped for retro_mmus_1907 retrocopy.

TSS

No TSS is located nearby retro_mmus_1907 retrocopy 5' end.

Lab

retro_mmus_1907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1907 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,