RetrogeneDB ID: retro_mmur_1421

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_56871:727..1672(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSMICG00000000192
• Aliases: None
• Description: spermine synthase [Source:HGNC Symbol;Acc:11123]

Sequence

>retro_mmur_1421
ATGGCAGCAGCACGGCACAGCACGCTCAACTTCATGCTCAGCGCCAAAGTTGATGGTGAGACCTTCTAAAAGGCCTCCAG
TCCAATTTCCAGGAGCAGGAGATGGCGGAGTTGGTGCATACCTGGCAGGACCATGAATATTTAGCAACTTACACAAACAA
AACTGGCAGCTTTGCCAATTTGAGAATTTACCCACATGGATGGGTGTTACGGGACCTTCAGAGGTACGACAGAGATGCAC
AGAGCAAGGAAGAAATTAACAGTCTCTTGAACAAAGTTGAAGAAAGAATGAAAGAACTGAACCAGGACAGTACTGGGTGG
ATGGAGTGATTACCACCCATAGTTCGAGGAGGGGCCGACAGATACTGGCCCACCGCTGATGGACGCCTGGTTGAATACGA
CATAGATGAAGTGGTGTATGATGAAGATTCACCTTATCAGAACACTAAAATTCTACACTTGAAGCAATTTGGAAATATTC
TCATCCCTCATAGTGGGGATGTTAATTTGGCAGAGAGTGACTTGGCGTATACTCAGGCCATCATGGACAGTGGCAAAGAA
GATAACACTGACAAAGACGTACTGATTCTGGGAGATGGAGATGGGGGCATATTATGTGAAATAGTCAAACTGAAACCAAA
GATGGTCGCTATGGTAGAAATTGACCAAATGGTGATTGATGGATGTAAGAAATATATGCGAAAAAATGTGCAGTGATGTC
TTAGACAATCTTAAAGGAGACTGCTATCAGGTTCTAATAGAAGACTGTATTCCAGTACTGAAGAGGTATGCCAAAGAAGG
GAGAGAGTTTGATTATGGGATTAATGATTTGACGGCTGTTCAAATCTCCACGTCTCCAGAAGAAGATTCCACATGGGAGT
TTCTCAGACTGATTCTTGACCTCTCCATGAAAGTATTGAAGCAGGATGGGAAATATTTCACACAG

Alignment

ORF - retro_mmur_1421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.05 %
• Parental protein coverage: 86.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAARHSTLD-MLGAKADGET-ILKGLQSIFQEQGMVESVHTWQDHGYLATYTNKNGSFANLRIYPHGLV
          MAAARHSTL..ML.AK.DGET..LKGLQS.FQEQ.M.E.VHTWQDH.YLATYTNK.GSFANLRIYPHG.V
Retrocopy MAAARHSTLNFMLSAKVDGET<LLKGLQSNFQEQEMAELVHTWQDHEYLATYTNKTGSFANLRIYPHGWV

Parental  LLDLQSYDTDAQSKEEIDTLLNKVEERMKELNQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEV
          L.DLQ.YD.DAQSKEEI..LLNKVEERMKELNQDSTG....LPPIVRGGA.DRYWPTADGRLVEYDIDEV
Retrocopy LRDLQRYDRDAQSKEEINSLLNKVEERMKELNQDSTGWME*LPPIVRGGA-DRYWPTADGRLVEYDIDEV

Parental  VYDEDSPYQNIKILHSKQFGNILI-LSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEI
          VYDEDSPYQN.KILH.KQFGNILI..SGDVNLAESDLAYT.AIM.SGKED.T.KDVLILG.GDGGILCEI
Retrocopy VYDEDSPYQNTKILHLKQFGNILIPHSGDVNLAESDLAYTQAIMDSGKEDNTDKDVLILGDGDGGILCEI

Parental  VKLKPKMVTMVEIDQMVIDGCKKYMRKT-CGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDL
          VKLKPKMV.MVEIDQMVIDGCKKYMRK..C.DVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDY.INDL
Retrocopy VKLKPKMVAMVEIDQMVIDGCKKYMRKN>CSDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYGINDL

Parental  TAVPISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQ
          TAV.ISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQ
Retrocopy TAVQISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1421 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1421 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus	ENSMICG00000000192	3 retrocopies	retro_mmur_1421 , retro_mmur_1484, retro_mmur_699,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458, retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,