RetrogeneDB ID: retro_mmus_24

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:72309320..72311159(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000053830
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Hbs1l
• Ensembl ID: ENSMUSG00000019977
• Aliases: Hbs1l, 2810035F15Rik, AI326327, eRFS
• Description: Hbs1-like (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1891704]

Sequence

>retro_mmus_24
ATGGCCCGGCATCGGAACGTCCGGGGATATAACTACGATGAAGATTTTGAAGATGATGATCTGTATGGGCAGTCTGTGGA
GGATGACTACTGTATCTCACCATCAACAGCCGCTCAGTTCATTTACTCACGCCGTGACAACCCTGAAGAAGAATATGGCT
ATGAAGATCTGAGAGAGTCTTCTAATTCTCTTTTGAATCACCAATTAAGTGAAATTGACCAAGCTCGCCTGTATTCATGC
CTTGATCACATGAGAGAGGTACTGGGGGACGCTGTGCCTGATGACATACTGACTGAGGCAATTCTGAAACACAAATTTGA
TGTGCAGAAGGCTTTGTCCGTGGTTCTGGAACAAGATGGTGTGCAGCCTTGGAAGGAGAAGAGTGAGCGAGCAGTGTGTG
CAGGACAGCCTTCAAAAGGAGTCTTATTTTCTTCCTTTGGAGTTTCACCCCAAAATGTTCACCATTCTTATCTTCAATCA
GAAAATCATTTGGATAGCAGTAGCAAACCTTTTGATTGTTGTAGCTCAATAGCAGAATATGGATCCCATAGTTCTTCACT
TGAGCCACGTCACTATTTACTTCATAGAAAAGAGAAACATGACAGACCCCAAAGTGAAAAGGAACTAGAATCATGTAAGT
TAACAAAAGAGCTGGCTCTAGCTCACCTGATTCATGATACGCCAAGAGATTCTTGTGCACGCCAGCTGTCAGCCAGACTG
CCACCCTCAGACAGCGGGCAGAGTGAGCTTCTTAAGAGCCTAGGTGCTGATGTGGTAAGACCTCCTGCATCTGCGTGTGC
TCCTGAAGAGGATTTTACTTTCAAAGGGATACGAGACTTAGAGTCCCTAGTGAGGGAGGACGTAGTAACTAGTGGTTCTT
TGGGAATTCGGAGCAGCTCACTACCTGATTTTCAAAGTACTCCCGTGCAGAACGTCTCAGCAAGCTTAAGTAATCCACTG
CTGTTATCTAGCCCAGTGGAAAATAATTCCAGTATAAACACTGAAGTTGAACAAAGTGCCAAGAATAATATTGTAAAAAC
TAACAGTTTACCATTTTCCCAGCGTGAAAGTCCATCCCTAGCTGAGCTGTTTGAGGAACACAGAGGAAGCAGCTCTGGCC
AGTGCTTTACTTTGTCTGACCTGTGTAACCAGTCACCTGCCAGCTTGGGTTCCCTTCCCCTGTCACAACTGGCAAACCGC
TCGCAGTCTGCTAACGGAGTATCAGAGTTAACAGGATCTCTGTCATCTTTGGCATTTTGTAAAGCTGCCCCCACGAGAGA
CCTGGAGAATTTATCCCTTTCTGATTTGATTGCAAAAACGATTGGACTAGACAATTCTCAGATTAACAGAGATTCCTTTG
AGTTTAGTTTATCTGAAACTATGAGGAGCCCTGAAGTTGATTCAAATATTGATCTTAGTGTCTTGATAAAAACTCCAGAG
TTTGTCCCAAAGCCTGTAGTTGACCCATCAGTTGCTGTAACACCAGACACTAAAGTTCTGAGTTCAAAGTTAGGGAAACC
TTCCAATTCTACTAAGGATAGTATGAAACCCAAAAGAGCCTCCCTTGCTAGGAAAGCTCCTCTGTCTCTGCCGTGGACCA
AGGCCCTTGCTGCTAGGCCTTCAGCTTTCGCGTCAACGCTGTGTCTTCGTTACCCACTGAAAAGCTGCAAGAGGCGCACT
CTTGAACTCTACAAGACTTTCCTTTATAGCAGACAAGTTCAAGATGTATCGGACAAAGAAATAAGTCCTCTTGCAGCAAT
AACGCCATTTGACTTCAAATCAGCATCTCCTGATGACGTTGTAAAAGCTAATCAAAAGAAGGCGTTTACTAGAGAATAG

Alignment

ORF - retro_mmus_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.84 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARHRNVRGYNYDEDFEDDDLYGQSVEDDYCISPSTAAQFIYSRRDNPEEEYGYEDLRESSNSLLNHQLS
          MARHRNVRGYNYDEDFEDDDLYGQSVEDDYCISPSTAAQFIYSRRDNPEEEYGYEDLRESSNSLLNHQLS
Retrocopy MARHRNVRGYNYDEDFEDDDLYGQSVEDDYCISPSTAAQFIYSRRDNPEEEYGYEDLRESSNSLLNHQLS

Parental  EIDQARLYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQDGVQPWKEKSERAVCAGQPSKG
          EIDQARLYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQDGVQPWKEKSERAVCAGQPSKG
Retrocopy EIDQARLYSCLDHMREVLGDAVPDDILTEAILKHKFDVQKALSVVLEQDGVQPWKEKSERAVCAGQPSKG

Parental  VLFSSFGVSPQNVHHSYLQSENHLDSSSKPFDCCSSIAEYGSHSSSLEPRHYLLHRKEKHDRPQSEKELE
          VLFSSFGVSPQNVHHSYLQSENHLDSSSKPFDCCSSIAEYGSHSSSLEPRHYLLHRKEKHDRPQSEKELE
Retrocopy VLFSSFGVSPQNVHHSYLQSENHLDSSSKPFDCCSSIAEYGSHSSSLEPRHYLLHRKEKHDRPQSEKELE

Parental  SCKLTKELALAHLIHDTPRDSCARQLSARLPPSDSGQSELLKSLGADVVRPPASACAPEEDFTFKGIRDL
          SCKLTKELALAHLIHDTPRDSCARQLSARLPPSDSGQSELLKSLGADVVRPPASACAPEEDFTFKGIRDL
Retrocopy SCKLTKELALAHLIHDTPRDSCARQLSARLPPSDSGQSELLKSLGADVVRPPASACAPEEDFTFKGIRDL

Parental  ESLVREDVVTSGSLGIRSSSLPDFQSTPVQNVSASLSNPLLLSSPVENNSSINTEVEQSAKNNIVKTNSL
          ESLVREDVVTSGSLGIRSSSLPDFQSTPVQNVSASLSNPLLLSSPVENNSSINTEVEQSAKNNIVKTNSL
Retrocopy ESLVREDVVTSGSLGIRSSSLPDFQSTPVQNVSASLSNPLLLSSPVENNSSINTEVEQSAKNNIVKTNSL

Parental  PFSQRESPSLAELFEEHRGSSSGQCFTLSDLCNQSPASLGSLPLSQLANRSQSANGVSELTGSLSSLAFC
          PFSQRESPSLAELFEEHRGSSSGQCFTLSDLCNQSPASLGSLPLSQLANRSQSANGVSELTGSLSSLAFC
Retrocopy PFSQRESPSLAELFEEHRGSSSGQCFTLSDLCNQSPASLGSLPLSQLANRSQSANGVSELTGSLSSLAFC

Parental  KAAPTRDLENLSLSDLIAKTIELDNSQINRDSFEFSLSETMRSPEVDSNIDLSVLIKTPEFVPKPVVDPS
          KAAPTRDLENLSLSDLIAKTI.LDNSQINRDSFEFSLSETMRSPEVDSNIDLSVLIKTPEFVPKPVVDPS
Retrocopy KAAPTRDLENLSLSDLIAKTIGLDNSQINRDSFEFSLSETMRSPEVDSNIDLSVLIKTPEFVPKPVVDPS

Parental  VAVTPDTKVLSSKLGKPSNSTKDSMKPKRASLARKAPLSLPWTKALAARPSAFASTLCLRYPLKSCKRRT
          VAVTPDTKVLSSKLGKPSNSTKDSMKPKRASLARKAPLSLPWTKALAARPSAFASTLCLRYPLKSCKRRT
Retrocopy VAVTPDTKVLSSKLGKPSNSTKDSMKPKRASLARKAPLSLPWTKALAARPSAFASTLCLRYPLKSCKRRT

Parental  LELYKTFLYSRQVQDVSDKEISPLAAITPFDFKSASPDDVVKANQKKAFTRE
          LELYKTFLYSRQVQDVSDKEISPLAAITPFDFKSASPDDVVKANQKKAFTRE
Retrocopy LELYKTFLYSRQVQDVSDKEISPLAAITPFDFKSASPDDVVKANQKKAFTRE

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	0.02 RPM	37.50 RPM
SRP007412_cerebellum	0.00 RPM	41.81 RPM
SRP007412_heart	0.03 RPM	54.82 RPM
SRP007412_kidney	0.08 RPM	51.34 RPM
SRP007412_liver	0.05 RPM	63.74 RPM
SRP007412_testis	0.00 RPM	121.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_24 was not detected

EST

15 EST(s) were mapped to retro_mmus_24 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA118417	72309297	72309732	99.1	431	4	427
AI787755	72309553	72309741	100	188	0	188
AV044672	72309584	72309818	95.8	224	10	214
BQ256447	72309217	72309885	100	668	0	668
BQ558855	72309658	72310061	100	403	0	403
BU559782	72309217	72309740	99.7	521	2	519
CA531941	72309658	72310228	100	570	0	570
CA949164	72309464	72309919	100	455	0	455
CD550387	72309228	72309740	100	512	0	512
CD550404	72309228	72309808	100	518	0	517
CD555716	72309219	72309736	100	517	0	517
CF172634	72309217	72309890	100	673	0	673
CF913648	72309217	72309853	100	636	0	636
CJ186546	72309200	72309808	100	432	0	430
CN691083	72309219	72309769	100	550	0	550

TSS

No TSS is located nearby retro_mmus_24 retrocopy 5' end.

Lab

retro_mmus_24 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_24 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000004802	1 retrocopy	retro_mmul_353,
Mus musculus	ENSMUSG00000019977	1 retrocopy	retro_mmus_24 ,
Mus musculus	ENSMUSG00000062203	1 retrocopy	retro_mmus_238,