RetrogeneDB ID: retro_mmus_3670

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:96224414..96225207(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081742
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Slc37a3
• Ensembl ID: ENSMUSG00000029924
• Aliases: Slc37a3, 2610507O21Rik, AU044904
• Description: solute carrier family 37 (glycerol-3-phosphate transporter), member 3 [Source:MGI Symbol;Acc:MGI:1919394]

Sequence

>retro_mmus_3670
TTAAAAGACAGTATTTCCAAGCAGTGGACCCCCAAATGTTTTTAGCATATCAGTTGGCCTGCCTGCAGAGATCTGGAGCA
GCAACCATCTGTTTCCCAGCACAGAGGAAGCCACTCTTTTTCTTGGAACACTAGATACTGTGTTTTTATTTTCCTGTGCT
GTGGGCCTCTTCATCAGTGGCATCATAGGGGATCAGCTGAATTTGCGACGGGTTCTGTCTTTTGGCATGTGCTCTTCTGT
ATTTGTGGTGTTTGTCTTTGGTATTCTTACGGAATGGCTGTACTTCTACAATAAGTGATTCTACTGTGGCCTGTGGATTG
TGAACGGTCTGCTGCAGTTCACTGGTTGGCCTTGTGTGGTTGCTGTGATGGGCAACTGGTTTGGGAAAGCTGGCTGAGGA
GTTGTCTTTGGACTCTGCAGTGCATATGCTTCAGGGGACAATATTTTGGGAGCATGCCTGGATTCATCGGTTCTCCAGTA
TGGTTATGAGTACACCTTTCTGGTGACTGCATCTGTGCAGTTTGCTGGTGGGACTTCTTTGGACTTCTCGTGTCACCAGA
AAAATATTGGTCTCCCAAGTATCAAGTCAGAGGAAAGCTTGGAAAAAGATTCACAGAGGCCACTCATCAATGGTGCTGAA
AATGAAGATGATTATGAGCCTAATTATTCAATCCAGGAGGACAGGTCTGTCATCCAAGTGAAGGCCATAAGCTTTCATCA
GGCTTGCTGCTTTCCTGGAGTCATACTGTACTCACTGGCCTACACCTGCCTGAATCTAGTGAATTACTACTTC

Alignment

ORF - retro_mmus_3670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.02 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKVSISKQWTP-NAFNTSLDLPAEIWSSNHLFPSTEEATLFLGTLDTVFLFSYAVGLFISGIIGDRLNLR
          .K.SISKQWTP.N.F..S..LPAEIWSSNHLFPSTEEATLFLGTLDTVFLFS.AVGLFISGIIGD.LNLR
Retrocopy LKDSISKQWTP>NVFSISVGLPAEIWSSNHLFPSTEEATLFLGTLDTVFLFSCAVGLFISGIIGDQLNLR

Parental  WVLSFGMCSSAFVVFVFGTLTEWLHFYNKWFYCGLWIVNGLLQSTGWPCVVAVMGNWFGKAGRGVVFGLW
          .VLSFGMCSS.FVVFVFG.LTEWL.FYNK.FYCGLWIVNGLLQ.TGWPCVVAVMGNWFGKAG.GVVFGL.
Retrocopy RVLSFGMCSSVFVVFVFGILTEWLYFYNK*FYCGLWIVNGLLQFTGWPCVVAVMGNWFGKAG*GVVFGLC

Parental  SACASVGNILGAFLASSVLQYGYEYAFLVTASVQFAGGIIIFFGLLVSPEEIGLPSIGAEESSEEDSQRP
          SA.AS..NILGA.L.SSVLQYGYEY.FLVTASVQFAGG....F........IGLPSI..EES.E.DSQRP
Retrocopy SAYASGDNILGACLDSSVLQYGYEYTFLVTASVQFAGGTSLDFS--CHQKNIGLPSIKSEESLEKDSQRP

Parental  LIDGAENEDDYEPNYSIQEDRAVVQVKAISFHQACCLPGVIPYSLAYACLKLVNYSF
          LI.GAENEDDYEPNYSIQEDR.V.QVKAISFHQACC.PGVI.YSLAY.CL.LVNY.F
Retrocopy LINGAENEDDYEPNYSIQEDRSVIQVKAISFHQACCFPGVILYSLAYTCLNLVNYYF

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	0.00 RPM	46.24 RPM
SRP007412_cerebellum	0.00 RPM	38.51 RPM
SRP007412_heart	0.00 RPM	18.49 RPM
SRP007412_kidney	0.00 RPM	48.01 RPM
SRP007412_liver	0.00 RPM	27.01 RPM
SRP007412_testis	0.00 RPM	10.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3670 was not detected

EST

No EST(s) were mapped for retro_mmus_3670 retrocopy.

TSS

No TSS is located nearby retro_mmus_3670 retrocopy 5' end.

Lab

retro_mmus_3670 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3670 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012239	1 retrocopy	retro_btau_1471,
Canis familiaris	ENSCAFG00000003973	1 retrocopy	retro_cfam_2207,
Mus musculus	ENSMUSG00000029924	1 retrocopy	retro_mmus_3670 ,
Ictidomys tridecemlineatus	ENSSTOG00000010929	1 retrocopy	retro_itri_1795,
Tursiops truncatus	ENSTTRG00000009525	1 retrocopy	retro_ttru_921,