RetrogeneDB ID: retro_mmus_2553

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:25450262..25450908(+)
• Located in intron of: ENSMUSG00000038056

Retrocopy information

• Ensembl ID: ENSMUSG00000092510
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Spag7
• Ensembl ID: ENSMUSG00000018287
• Aliases: Spag7, 5730443G10, ACRP, FSA-1, Fsa1l
• Description: sperm associated antigen 7 [Source:MGI Symbol;Acc:MGI:107380]

Sequence

>retro_mmus_2553
CTCACGCCCCTCTCACCCAGTCCCAAGATGGCAGACCTATTGGTAAGGCCGGAGAGCAGACTGCCTGCCTGAAGAAACTA
CAAGAGCAAGAAAGATATACAGCAAAAAGTGGAGTTTCATAAAAGGATGGAGAAAGAGGTGTCTGGTTTCATCCAGGACA
GTGAACAGATCAAGAAAAAGTTTCAGCCTATGAACAAGAAAGAGAGAGTGGAGCATACTACATGATGTGGTAGAGGTAGC
TGGCCTCACATCCTTCTCCTTTGGAGAAGATGATGACTGTCACTATACCATGATCTTCAAAAAAGGGTTTGCACCCTCAG
ATGAAGGGCTAGACTGCTACCGTCATAGAGAGGCATGGGACCCCCCCAGAAGGCTGAGGAGAAGCAGAAGCTAAGGAGTT
AGCTCAGAAGCAGGAGGAAGATGCAGCGCAGCAGGGAACCACGGTTGTGAGTCTTCCAGCAACTACAGGACAAGTATTGG
CAAAGGAGCAGCCAAAGATGCAGCCTACATGCTACAGGCCAACAAGACCTATGGCTGTGTGCCTGTGGCCAACAAGTGGG
ACACATGCTCCATAGAAGAGGCCATGAATGAGATCAGAGCCAAATAATGTCTGCAGCAGAGTGGGGAAGAGTTGTCAACT
ACCTCC

Alignment

ORF - retro_mmus_2553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.33 %
• Parental protein coverage: 96.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSSMEKPPSLGDQESRRKAREQAARLKKLQEQDKQQKVEFRKRMEKEVSDFIQDSGQV-KKKFQP-MNKI
          L......P...D...R...R..A.R..K....D.QQKVEF.KRMEKEVS.FIQDS.Q...K.F.....K.
Retrocopy LTPLSPSPKMADLLVRPESRLPA*RNYK-SKKDIQQKVEFHKRMEKEVSGFIQDSEQI>RKSFSL*TRKR

Parental  ERSILHDVVEVAGLTSFSFGEDDDCRYVMIFKKEFAPSDEELDSYRHGEEWDPQKAEEKRK-LKELAQKQ
          E.SILHDVVEVAGLTSFSFGEDDDC.Y.MIFKK.FAPSDE.LD.YRH.E.WDP..........KELAQKQ
Retrocopy EWSILHDVVEVAGLTSFSFGEDDDCHYTMIFKKGFAPSDEGLDCYRHREAWDPPRRLRRSR>AKELAQKQ

Parental  EEEAAQQGPAVVS-PASDYKDKYSHLIGKGAAKDAAHMLQANKTYGCVPVANKRDTRSIEEAMNEIRAKK
          EE.AAQQG..VVS...S.Y.........K.AA.....MLQANKTYGCVPVANK.DT.SIEEAMNEIRAK.
Retrocopy EEDAAQQGTTVVS<SSSNYRTSIGKGAAKDAA----YMLQANKTYGCVPVANKWDTCSIEEAMNEIRAK*

Parental  RLRQSGEELPTTS
          .L.QSGEEL.TTS
Retrocopy CLQQSGEELSTTS

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	25.63 RPM
SRP007412_cerebellum	0.04 RPM	36.43 RPM
SRP007412_heart	0.00 RPM	63.54 RPM
SRP007412_kidney	0.04 RPM	45.37 RPM
SRP007412_liver	0.05 RPM	21.71 RPM
SRP007412_testis	0.00 RPM	34.03 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2553 was not detected

EST

No EST(s) were mapped for retro_mmus_2553 retrocopy.

TSS

No TSS is located nearby retro_mmus_2553 retrocopy 5' end.

Lab

retro_mmus_2553 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2553 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006299	1 retrocopy	retro_amel_964,
Canis familiaris	ENSCAFG00000015761	1 retrocopy	retro_cfam_1417,
Dasypus novemcinctus	ENSDNOG00000011669	1 retrocopy	retro_dnov_1149,
Echinops telfairi	ENSETEG00000020098	1 retrocopy	retro_etel_1489,
Felis catus	ENSFCAG00000030469	1 retrocopy	retro_fcat_833,
Macropus eugenii	ENSMEUG00000007933	1 retrocopy	retro_meug_1358,
Myotis lucifugus	ENSMLUG00000014031	1 retrocopy	retro_mluc_1561,
Mus musculus	ENSMUSG00000018287	1 retrocopy	retro_mmus_2553 ,
Oryctolagus cuniculus	ENSOCUG00000001108	1 retrocopy	retro_ocun_1103,