RetrogeneDB ID: retro_mmus_2803

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:10774135..10774726(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pa2g4
• Ensembl ID: ENSMUSG00000025364
• Aliases: Pa2g4, 38kDa, AA672939, Ebp1, Plfap
• Description: proliferation-associated 2G4 [Source:MGI Symbol;Acc:MGI:894684]

Sequence

>retro_mmus_2803
TTGGAAGCTATGCTTTCACAACAATGGAAGTAGCATGTGATCCATGAAAAGAAAATGGTTATCCAGAATCCTACAGATCA
GCAGACAGACCATGTAAATTGTGAATTCAAGATGCATGTAGTTTATGCTGTGGGTGGCTCTCTGGCTAAGGAGAAGGCAA
GATCAAAGATTCCAGGGCAGAGAACCATCATTTACAAAGAAAACCCATCTCAACAATATGGCCTGAAAATGATGTTGTCA
CATGCCTTTTTTCAGTGGTGTAGAAAGAGGTTTTGATCTGTGCTTTTAGTTCAAGAGTATTTGAAAATGAAAACGCTAGA
CTGAGTGTGGTCAAGTGTGCCAAATGTGACCTACTACACCCTTTTACTACTCTCTAAACAAGGAGGGTGAATTTGCTGCC
CAGTTTAAATTTACATCACCCATCCACAATGGCCCCATGTGGATAACAGTGGGCCCTTTGAGCTTGACCTCTATAAATCT
GAGGTGGAGGTGAGGTCCAGGATGCAGAGTTAAAGGCTCTTCTCAGACTTCTACAAGTTGAAAGACTCAAACAAAGCAAA
AATGAAAAAGAAGGTCTCTAAAACTGTGGAG

Alignment

ORF - retro_mmus_2803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.96 %
• Parental protein coverage: 50.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IEGMLSHQLKQHVIDGEKTIIQNPTDQQKKDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDP
          .E.MLS.Q.K.HVI...K..IQNPTDQQ..DH...EF..H.VYAV...........K..GQRT.IYK..P
Retrocopy LEAMLSQQWK*HVIHEKKMVIQNPTDQQT-DHVNCEFKMHVVYAVGGSLAKEKARSKIPGQRTIIYKENP

Parental  SKQYGLKMKTSRAFFSEVERRFDAM-PFTLRAFEDEKKARMGVVECAKHELLQPFNVL-YEKEGEFVAQF
          S.QYGLKM..S.AFF.....RF.....F..R.FE.E..AR..VV.CAK..LL.PF..L...KEGEF.AQF
Retrocopy SQQYGLKMMLSHAFFQWCRKRF*SV<AFSSRVFENE-NARLSVVKCAKCDLLHPFTTL<LNKEGEFAAQF

Parental  KFTVLLMPNGPMRIT-SGPFEPDLYKSEMEVQDAELKALLQSSASRKTQKKKKK---KASKTVE
          KFT.....NGPM.IT.SGPFE.DLYKSE.EV........L.S.........K.K...K.SKTVE
Retrocopy KFTSPI-HNGPMWIT<SGPFELDLYKSEVEVRSRMQS*RLFSDFYKLKDSNKAKMKKKVSKTVE

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	59.76 RPM
SRP007412_cerebellum	0.00 RPM	62.09 RPM
SRP007412_heart	0.00 RPM	50.15 RPM
SRP007412_kidney	0.00 RPM	67.95 RPM
SRP007412_liver	0.00 RPM	80.31 RPM
SRP007412_testis	0.00 RPM	83.75 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2803 was not detected

EST

No EST(s) were mapped for retro_mmus_2803 retrocopy.

TSS

No TSS is located nearby retro_mmus_2803 retrocopy 5' end.

Lab

retro_mmus_2803 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2803 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803 ,
Mus musculus	ENSMUSG00000036112	2 retrocopies	retro_mmus_3689, retro_mmus_770,
Oryctolagus cuniculus	ENSOCUG00000017342	1 retrocopy	retro_ocun_1733,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Tarsius syrichta	ENSTSYG00000006777	1 retrocopy	retro_tsyr_746,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,