RetrogeneDB ID: retro_mmus_2162

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:58652052..58653156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sms
• Ensembl ID: ENSMUSG00000071708
• Aliases: Sms, AI427066, Gy, SPMSY, SpmST, gyro
• Description: spermine synthase [Source:MGI Symbol;Acc:MGI:109490]

Sequence

>retro_mmus_2162
ATGGCAGCAGCAAGACACAGCATGCTAGACTTCACGCTGGGTGCCAAAGCTGATGGTGAGGCCATTCTGAAAGGCCTTCA
GTCCAGTTTTTTCAGGAGCAGGGGATGACAGAGTCAGTGCACACCTGGCAGGACCATGGATATTTAGCAACTTACACGAA
CAAGAATGGCAGCTTTGCCAATGTGCGAATTTATCCACATGGATTGGTGTTGCTGGACCTTCAGAGTTACGACAGTGATG
TGCAAGGCAAACAAGAAACTGACAACCTTTTGAACAAGATAGAAGAAAAAAATGAAAGAATTGAGTCAAGACAGTACAGG
GCGGGTGAAGCGATTACCACCCATAGTTCGAGGAGGGGCTGTTGACAGATACTGGCCTACTGCTGATGGGCGCCTGGTTG
AGTATGACGTAGATGAAGTAGTGTATGATGAAGATTCACCCTATCAGAACATTAAAATCCTACACTCAGAGCAGTTTGGG
AATATTCTCATCCTCAGCGGGGATGTTAATTTGGCAGAGAGTGACTTGGCATATACTCGGGCCAACATGGGCAGTGGTAA
AGAAGACTACACTGGCAAAGATACACGGATTCTGGGAGGTGGGGATGGAGGCATATTGTGTGAAATTGTCAAACTGGAAC
CAAAGATGGTCACTATGGTAGAGATTGACCAAATGGTCACTGATGGATGTAAGAAATACATGCGGAGAACATGTGGAGAT
GTCTTAGGCAATCTTAAAGGAGACTGCTATCAGGGTCTTATAGAAGACTGCAACCCAGTTCTGAAGAGGTAAGCCAAAGA
AGGGAGAGAGTTTGATTATGTGACTAGTGATTTGACAGATAGCTGTCCCTAACTCTATTCTCCAGAAGAAGATTGCACAT
GGGAGTTCCTCAGACTGATTCTCGACCTGTCAATGAAGGTTCTGAAACAGGATGGAAAATACTTCACACAGAGGAACTGT
GTCAACTTGACTGAAGCCCTGTCGCTCTATGAAGAACAGCTGGGGCATCTGTATTGTCCTGTGGAATTCTCAAAAGAGAT
TGTCTGTGTCCCCTCATACTTGGAATTGTGGGTATTTTACACTGTTTGGAAGAAAGCTAAGCCT

Alignment

ORF - retro_mmus_2162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAARHSTLDFKLGAKADGEAILKGLQS-IFQEQG-MTESVHTWQDHGYLATYTNKNGSFANLRIYPHGL
          MAAARHS.LDF.LGAKADGEAILKGLQS..F...G.MTESVHTWQDHGYLATYTNKNGSFAN.RIYPHGL
Retrocopy MAAARHSMLDFTLGAKADGEAILKGLQSSFFRSRG<MTESVHTWQDHGYLATYTNKNGSFANVRIYPHGL

Parental  VLLDLQSYDSDVQGKQETDSLLNKIEE-KMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDID
          VLLDLQSYDSDVQGKQETD.LLNKIEE.KMKELSQDSTGRVKRLPPIVRGGA.DRYWPTADGRLVEYD.D
Retrocopy VLLDLQSYDSDVQGKQETDNLLNKIEE>KMKELSQDSTGRVKRLPPIVRGGAVDRYWPTADGRLVEYDVD

Parental  EVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCE
          EVVYDEDSPYQNIKILHS.QFGNILILSGDVNLAESDLAYTRA.MGSGKEDYTGKD..ILGGGDGGILCE
Retrocopy EVVYDEDSPYQNIKILHSEQFGNILILSGDVNLAESDLAYTRANMGSGKEDYTGKDTRILGGGDGGILCE

Parental  IVKLKPKMVTMVEIDQMVIDGCKKYMRRTCGDVLDNLRGDCYQVLIEDCIPVLKMYAKEGREFDYVINDL
          IVKL.PKMVTMVEIDQMV.DGCKKYMRRTCGDVL.NL.GDCYQ.LIEDC.PVLK..AKEGREFDYV..DL
Retrocopy IVKLEPKMVTMVEIDQMVTDGCKKYMRRTCGDVLGNLKGDCYQGLIEDCNPVLKR*AKEGREFDYVTSDL

Parental  T-AVPISTSPEEDSTWDFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIV
          T...P...SPEED.TW.FLRLILDLSMKVLKQDGKYFTQ.NCVNLTEALSLYEEQLG.LYCPVEFSKEIV
Retrocopy TDSCP*LYSPEEDCTWEFLRLILDLSMKVLKQDGKYFTQRNCVNLTEALSLYEEQLGHLYCPVEFSKEIV

Parental  CVPSYLELWVFYTVWKKAKP
          CVPSYLELWVFYTVWKKAKP
Retrocopy CVPSYLELWVFYTVWKKAKP

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	0.40 RPM	66.02 RPM
SRP007412_cerebellum	0.35 RPM	67.91 RPM
SRP007412_heart	0.06 RPM	24.97 RPM
SRP007412_kidney	0.21 RPM	31.51 RPM
SRP007412_liver	0.00 RPM	2.79 RPM
SRP007412_testis	0.32 RPM	2.24 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2162 was not detected

EST

No EST(s) were mapped for retro_mmus_2162 retrocopy.

TSS

No TSS is located nearby retro_mmus_2162 retrocopy 5' end.

Lab

retro_mmus_2162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2162 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 41 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,
Homo sapiens	ENSG00000102172	5 retrocopies	retro_hsap_243, retro_hsap_3168, retro_hsap_3193, retro_hsap_3611, retro_hsap_4826,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Macaca mulatta	ENSMMUG00000020392	2 retrocopies	retro_mmul_2003, retro_mmul_2574,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Mus musculus	ENSMUSG00000071708	6 retrocopies	retro_mmus_2162 , retro_mmus_2170, retro_mmus_2837, retro_mmus_3502, retro_mmus_3628, retro_mmus_994,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
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,