RetrogeneDB ID: retro_mmus_3678

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:103163112..103164474(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000048949
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rfwd2
• Ensembl ID: ENSMUSG00000040782
• Aliases: Rfwd2, AI316802, C80879, Cop1
• Description: ring finger and WD repeat domain 2 [Source:MGI Symbol;Acc:MGI:1347046]

Sequence

>retro_mmus_3678
CAATTGGAGCAGATCCAGAAGGAACTAAGTGTTTTGGAAGAGGATATTAAAAGAGTGGAAGAAATGAGTGGCCTCTACTC
TCCTGTCAGTGAAGATAGCACAGTGCCTCAATTTGAAGCTCCTTCTCCATCACACAGTAGCATTATTGATTCTACAGAAT
ATAGCCAACCTCCAGGTTTCAGTGGGACCTCTCAGACAAAGAAACAGCCTTGGTATAACAGCACATTAGCATCAAGACGA
AAGCGACTCACTGCTCATTTTGAAGACTTAGAGCAGTGTTATTTTTCTACAAGGATGTCTCGTATCTCAGATGACAGTAG
AACTGCAAGCCAGTTAGATGAATTTCAAGAATGCTTGTCCAAGTTTACTCGATACAACTCAGTAAGACCGTTGGCCACAT
TGTCTTATGCTAGTGATCTCTATAATGGTTCCAGCATAGTTTCTAGTATTGAGTTTGACCGGGATTGTGACTATTTTGCA
ATTGCTGGAGTTACAAAGAAGATTAAAGTCTATGAGTATGGCACAGTCATCCAGGATGCAGTGGATATTCATTACCCTGA
GAATGAAATGACCTGCAATTCCAAAATCAGCTGTATCAGTTGGAGTAGTTACCATAAGAACCTGCTAGCCAGCAGTGATT
ATGAAGGCACTGTTATACTATGGGATGGATTCACAGGACAGAGGTCAAAGGTCTATCAGGAGCATGAAAAAAGGTGTTGG
AGTGTTGACTTTAATCTGATGGATCCTAAACTTCTGGCTTCAGGTTCTGATGATGCAAAAGTGAAGCTGTGGTCTACCAA
TTTAGACAATTCTGTGGCGAGCATTGAGGCAAAGGCTAACGTGTGCTGTGTGAAGTTCAGCCCCTCCTCCAGGTACCATC
TGGCTTTCGGCTGTGCAGATCACTGTGTCCACTACTACGACCTTCGTAACACTAAACAGCCAATAATGGTATTCAAGGGA
CACCGAAAAGCAGTGTCTTATGCCAAGTTTGTGAGTGGTGAAGAAATTGTCTCAGCCTCAACAGACAGCCAACTAAAGCT
GTGGAATGTGGGAAAACCATACTGTCTACGTTCCTTCAAGGGTCATATTAATGAAAAAAACTTTGTAGGCCTTGCTTCCA
ATGGAGATTATATAGCGTGTGGAAGTGAGAACAACTCCCTCTACCTGTATTATAAAGGACTTTCTAAAACTTTGCTAACT
TTTAAGTTTGATACCGTTAAGAGTGTATTAGACAAAGATCGGAAAGAAGATGACACAAATGAATTTGTCAGTGCTGTGTG
TTGGCGGGCACTATCAGACGGGGAGTCCAATGTGCTGATTGCTGCTAACAGCCAGGGTACAATTAAGGTGCTAGAATTGG
TA

Alignment

ORF - retro_mmus_3678 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 61.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLEQIQKELSVLEEDIKRVEEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGTSQTKKQP
          QLEQIQKELSVLEEDIKRVEEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGTSQTKKQP
Retrocopy QLEQIQKELSVLEEDIKRVEEMSGLYSPVSEDSTVPQFEAPSPSHSSIIDSTEYSQPPGFSGTSQTKKQP

Parental  WYNSTLASRRKRLTAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDL
          WYNSTLASRRKRLTAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDL
Retrocopy WYNSTLASRRKRLTAHFEDLEQCYFSTRMSRISDDSRTASQLDEFQECLSKFTRYNSVRPLATLSYASDL

Parental  YNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYGTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLA
          YNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYGTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLA
Retrocopy YNGSSIVSSIEFDRDCDYFAIAGVTKKIKVYEYGTVIQDAVDIHYPENEMTCNSKISCISWSSYHKNLLA

Parental  SSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN
          SSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN
Retrocopy SSDYEGTVILWDGFTGQRSKVYQEHEKRCWSVDFNLMDPKLLASGSDDAKVKLWSTNLDNSVASIEAKAN

Parental  VCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNV
          VCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNV
Retrocopy VCCVKFSPSSRYHLAFGCADHCVHYYDLRNTKQPIMVFKGHRKAVSYAKFVSGEEIVSASTDSQLKLWNV

Parental  GKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTN
          GKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTN
Retrocopy GKPYCLRSFKGHINEKNFVGLASNGDYIACGSENNSLYLYYKGLSKTLLTFKFDTVKSVLDKDRKEDDTN

Parental  EFVSAVCWRALSDGESNVLIAANSQGTIKVLELV
          EFVSAVCWRALSDGESNVLIAANSQGTIKVLELV
Retrocopy EFVSAVCWRALSDGESNVLIAANSQGTIKVLELV

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	0.54 RPM	19.27 RPM
SRP007412_cerebellum	0.78 RPM	13.29 RPM
SRP007412_heart	0.25 RPM	19.58 RPM
SRP007412_kidney	0.87 RPM	16.17 RPM
SRP007412_liver	0.44 RPM	12.62 RPM
SRP007412_testis	1.65 RPM	23.51 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3678 was not detected

EST

No EST(s) were mapped for retro_mmus_3678 retrocopy.

TSS

No TSS is located nearby retro_mmus_3678 retrocopy 5' end.

Lab

retro_mmus_3678 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3678 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000013437	1 retrocopy	retro_ggor_1366,
Macaca mulatta	ENSMMUG00000002072	1 retrocopy	retro_mmul_1342,
Mus musculus	ENSMUSG00000031353	1 retrocopy	retro_mmus_3529,
Mus musculus	ENSMUSG00000040782	1 retrocopy	retro_mmus_3678 ,
Mus musculus	ENSMUSG00000057236	1 retrocopy	retro_mmus_356,
Nomascus leucogenys	ENSNLEG00000015420	1 retrocopy	retro_nleu_1225,
Pan troglodytes	ENSPTRG00000001711	1 retrocopy	retro_ptro_1281,