RetrogeneDB ID: retro_mmus_1580

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:55247729..55248636(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 4833439L19Rik
• Ensembl ID: ENSMUSG00000025871
• Aliases: 4833439L19Rik, 4930558H15Rik, C81457, Kiaa1191, P33monox
• Description: RIKEN cDNA 4833439L19 gene [Source:MGI Symbol;Acc:MGI:1921162]

Sequence

>retro_mmus_1580
ATGGTTTCAAGACAACCAGAAGTGCTTGCTCTTGCTCCCAGTGGGCCTCTAGGCAAGATGTCCCTGCCCATCGGGATGTG
CCACCGGGCATTTAGCTATGATGATGATGCCCTAGAGGACCCTGCACCCATGACTCCTCCTCCATCAGACATTTGCAGCA
TCCCCTGGAAGCCAGTAATTACAGAATGCAAGTATCAACATCTTGACAAGACAGAGGAAGGAACAGCCAGTGTCTCTTTC
CTTGCTGTGACTCCATCACCAGCTACTGACAGTTCAGACAAAGCCCTTCTGGTGAAGGCTAAAGCTACCCATGTCATCAA
TGAATTCCCTGATGGAAAAACAGACCCAAGAGAGCATGTAGTGTTTTGAACAACAGGCAGGACTGAGAGTTGCTAGCTAC
ACACCCCATAAGGGCCTTACCACAGAGGAGACCAAGTACCTTTGAGTGGCAGAAGCACTCCGTAAACTAAAGCTGCAGAG
TGGAGAGACAGCAAAAGAAGAGAAGCGCCCTGCATCAGCCCAGTCCACCCCGAGCAGCATCCCTCACTCGTCCCCTAAGC
AGAAGTCCAGGGGCTGGTTCCCATCTGGCTCCTCCACAGCCTTACCTGATCTGAATATCATAGATCTTGGGAGTGGAAAT
GATAGGAATTCAGCAGACAAATGGAGCATCTTTAGACCATGACCCCTGCAGAAATCTGATTCTGGTTTTGCTATTCAGGT
TTACAAAGGTGCCCCCAAACCCTCTCCTATGGAGGTGATGCATACCCAGGCCACACGAGTAGGTGAAGATCCAGCAACCT
TTAAGCCGCCAAAGATGGATGTCCCAATGGTAGAAGGAAAGAAACAACCACTTCGAACCCATAATCTCAAACCCCGTGAC
CTGAATGTGCTCACACCCACTGGCTTC

Alignment

ORF - retro_mmus_1580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.89 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASRQPEVPALAPSGPLGKMSLPIGMCRRAFSYDD-ALEDPAPMTPPPSDMGSIPWKPVIPERKYQHLDK
          M.SRQPEV.ALAPSGPLGKMSLPIGMC.RAFSYDD.ALEDPAPMTPPPSD..SIPWKPVI.E.KYQHLDK
Retrocopy MVSRQPEVLALAPSGPLGKMSLPIGMCHRAFSYDDDALEDPAPMTPPPSDICSIPWKPVITECKYQHLDK

Parental  TEEGAASVSSLAVTPSPATDSSDKAPVVKAKATHVI-MSSLITKQTQESIQRFEQQAGLRDAGYTPHKGL
          TEEG.ASVS.LAVTPSPATDSSDKA..VKAKATHVI.M.SL..KQTQES...FEQQAGLR.A.YTPHKGL
Retrocopy TEEGTASVSFLAVTPSPATDSSDKALLVKAKATHVI>MNSLMEKQTQESM*CFEQQAGLRVASYTPHKGL

Parental  TTEETKYLRVAEALHKLKLQSGETAKEEKHPASAQSTPSSTPHASPKQKSRGWFPSGSSTALPAPNPHTM
          TTEETKYL.VAEAL.KLKLQSGETAKEEK.PASAQSTPSS.PH.SPKQKSRGWFPSGSSTALP..N....
Retrocopy TTEETKYL*VAEALRKLKLQSGETAKEEKRPASAQSTPSSIPHSSPKQKSRGWFPSGSSTALPDLN--II

Parental  DPGSGNDRNSADKWSLFGPRPLQKSDSGFAIQAYKGAPRPSPMEVMRAQATRVGEDPATFKPPKMDVPMV
          D.GSGNDRNSADKWS.F.P.PLQKSDSGFAIQ.YKGAP.PSPMEVM..QATRVGEDPATFKPPKMDVPMV
Retrocopy DLGSGNDRNSADKWSIFRP*PLQKSDSGFAIQVYKGAPKPSPMEVMHTQATRVGEDPATFKPPKMDVPMV

Parental  EGKKQPLRTHNLKPRDLNVLTPTGF
          EGKKQPLRTHNLKPRDLNVLTPTGF
Retrocopy EGKKQPLRTHNLKPRDLNVLTPTGF

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	107.05 RPM
SRP007412_cerebellum	0.00 RPM	119.76 RPM
SRP007412_heart	0.00 RPM	87.41 RPM
SRP007412_kidney	0.12 RPM	539.18 RPM
SRP007412_liver	0.00 RPM	63.30 RPM
SRP007412_testis	0.00 RPM	39.47 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1580 was not detected

EST

No EST(s) were mapped for retro_mmus_1580 retrocopy.

TSS

No TSS is located nearby retro_mmus_1580 retrocopy 5' end.

Lab

retro_mmus_1580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1580 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006123	4 retrocopies	retro_chof_1411, retro_chof_1751, retro_chof_2197, retro_chof_959,
Callithrix jacchus	ENSCJAG00000012337	2 retrocopies	retro_cjac_1699, retro_cjac_901,
Cavia porcellus	ENSCPOG00000019402	1 retrocopy	retro_cpor_625,
Dasypus novemcinctus	ENSDNOG00000002676	3 retrocopies	retro_dnov_2220, retro_dnov_753, retro_dnov_976,
Equus caballus	ENSECAG00000003238	1 retrocopy	retro_ecab_621,
Felis catus	ENSFCAG00000007189	1 retrocopy	retro_fcat_1625,
Homo sapiens	ENSG00000122203	4 retrocopies	retro_hsap_1641, retro_hsap_3089, retro_hsap_524, retro_hsap_817,
Gorilla gorilla	ENSGGOG00000023834	4 retrocopies	retro_ggor_1240, retro_ggor_2122, retro_ggor_482, retro_ggor_669,
Loxodonta africana	ENSLAFG00000028878	1 retrocopy	retro_lafr_313,
Myotis lucifugus	ENSMLUG00000003498	1 retrocopy	retro_mluc_667,
Macaca mulatta	ENSMMUG00000003921	3 retrocopies	retro_mmul_1082, retro_mmul_1566, retro_mmul_1971,
Monodelphis domestica	ENSMODG00000005274	6 retrocopies	retro_mdom_116, retro_mdom_1992, retro_mdom_218, retro_mdom_56, retro_mdom_722, retro_mdom_751,
Mustela putorius furo	ENSMPUG00000012579	1 retrocopy	retro_mputfur_1237,
Mus musculus	ENSMUSG00000025871	2 retrocopies	retro_mmus_1580 , retro_mmus_737,
Nomascus leucogenys	ENSNLEG00000012473	4 retrocopies	retro_nleu_1327, retro_nleu_2233, retro_nleu_251, retro_nleu_2578,
Oryctolagus cuniculus	ENSOCUG00000012191	3 retrocopies	retro_ocun_1263, retro_ocun_1415, retro_ocun_1509,
Otolemur garnettii	ENSOGAG00000008281	6 retrocopies	retro_ogar_1543, retro_ogar_1986, retro_ogar_2289, retro_ogar_3002, retro_ogar_3075, retro_ogar_781,
Procavia capensis	ENSPCAG00000008839	1 retrocopy	retro_pcap_277,
Pongo abelii	ENSPPYG00000016068	4 retrocopies	retro_pabe_223, retro_pabe_2558, retro_pabe_2615, retro_pabe_729,
Pan troglodytes	ENSPTRG00000017558	5 retrocopies	retro_ptro_1111, retro_ptro_2086, retro_ptro_2975, retro_ptro_392, retro_ptro_568,
Pteropus vampyrus	ENSPVAG00000012448	1 retrocopy	retro_pvam_118,
Rattus norvegicus	ENSRNOG00000017133	2 retrocopies	retro_rnor_968, retro_rnor_969,
Ictidomys tridecemlineatus	ENSSTOG00000000946	2 retrocopies	retro_itri_1163, retro_itri_960,
Tupaia belangeri	ENSTBEG00000013189	1 retrocopy	retro_tbel_2271,
Tursiops truncatus	ENSTTRG00000005376	1 retrocopy	retro_ttru_383,