RetrogeneDB ID: retro_mmus_3501

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:103529694..103530116(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ebag9
• Ensembl ID: ENSMUSG00000022339
• Aliases: Ebag9, AI835379, Rcas1
• Description: estrogen receptor-binding fragment-associated gene 9 [Source:MGI Symbol;Acc:MGI:1859920]

Sequence

>retro_mmus_3501
ATCGAAGGAGGGAATGGGATTGTGGCAACACAGCAGAACTCTTTGGAGCAACTGGAACCTGACTACTTCGAGGCCATAAC
TCCAACTATACAGAAAACTCAGAAAATTGTCATTAAGAAGAGAGAACCATTGAATTTTGGTGTCCCAGATGGTAGCACAG
GTTTTTCCAGTAGATTGGCAGCTGCACAAGATAGGCCTTTTATTCATCAGTCTTCAAAATTAGGTGACTTAGATACGTGG
CAAGAAAATACCAGTGCATGGGAAGAGGAAGAAGACGCAGCCTGGCAAGCAGAAGAAGTCCTGAAGCAGCAGAAAATTTC
AGACGGAGAGAAGAGACAGCAGAACAACAAAGGAAGAAAACGGAGAAGGAAGCGCAACGCCCTATAAAGAAGGAGCAAAG
CAAAGTCTGTGTGAAGCTTTCC

Alignment

ORF - retro_mmus_3501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.21 %
• Parental protein coverage: 66.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IEGGNGNVATQQNSLEQLEPDYFKDMTPTIRKTQKIVIKKREPLNFGVPDGSTGFSSRLAATQDMPFIHQ
          IEGGNG.VATQQNSLEQLEPDYF...TPTI.KTQKIVIKKREPLNFGVPDGSTGFSSRLAA.QD.PFIHQ
Retrocopy IEGGNGIVATQQNSLEQLEPDYFEAITPTIQKTQKIVIKKREPLNFGVPDGSTGFSSRLAAAQDRPFIHQ

Parental  SSELGDLDTWQENSNAWEEEEDAAWQAEEVLRQQKIADREKR-AAEQQRKKMEKEAQRLMKKEQNKIGVK
          SS.LGDLDTWQEN..AWEEEEDAAWQAEEVL.QQKI.D.EKR..AEQQRKK.EKEAQR..KKEQ.K..VK
Retrocopy SSKLGDLDTWQENTSAWEEEEDAAWQAEEVLKQQKISDGEKR<TAEQQRKKTEKEAQRPIKKEQSKVCVK

Parental  LS
          LS
Retrocopy LS

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	1.03 RPM	16.54 RPM
SRP007412_cerebellum	0.83 RPM	16.54 RPM
SRP007412_heart	0.31 RPM	16.16 RPM
SRP007412_kidney	0.40 RPM	27.83 RPM
SRP007412_liver	0.33 RPM	22.37 RPM
SRP007412_testis	0.05 RPM	37.69 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_3501 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	X:103529048..103529665
ENCFF001YKA	POLR2A	X:103529022..103529681

EST

No EST(s) were mapped for retro_mmus_3501 retrocopy.

TSS

No TSS is located nearby retro_mmus_3501 retrocopy 5' end.

Lab

retro_mmus_3501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3501 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211, retro_ecab_232,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501 ,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,