RetrogeneDB ID: retro_mmus_287

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:3531794..3532711(+)
• Located in intron of: ENSMUSG00000051951

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slc35e3
• Ensembl ID: ENSMUSG00000060181
• Aliases: Slc35e3, 9330166G04Rik, AI481200
• Description: solute carrier family 35, member E3 [Source:MGI Symbol;Acc:MGI:2448489]

Sequence

>retro_mmus_287
ATGGCATCGTTGGCAGACCGGGTCTGGGGCAACAGGCGCATCGCCGCCGGGCTCCTGTTCAATCTGCTGGTGTCCATCTG
CATCGTGTTCCTCAACAAATGGATCTATGTACACCACGCTTCCCCAAGATGAGCCTGACACTGGTGCACGTCATGGTCAC
CTGGCTGGGCTTGTACATCTACCAGAAACTGGACATCTTTGCCCTTAAAAATCTGCCGCTCTCCAAGCTCCTCCTCCTGG
CCCTCAGCTTCTGTGGCTTTGTGGTCTTCACCAAACTTTCTCTGCAGAACAACACCATAGGCATCTATCAGCTGGCCAAG
GCCATGACCACGCCGGTTATCATAGCCATCCAAACCTTCTGGTACCAGAAGAGATTCTCCATCAGAATACAGCTCACCCT
GATTCCTATTACTGTAGGTGTAATCCTAAATTCTTATTACGACCTGAAGTTTCATTCCCTTGGAATGGTGTTTGCCACCC
TTGGTGTGGTAGTCACGTCCCTTTAACAAGTGTGGGTCGGAGCCAAGCAGCACGAACTGCAGGTGAACTCCATACAGCTA
CTTTACTACCAGGCCCCCGTGTCTTCCACCATGCTGCTGGTGGCTGTGCACTTCTTCGAGCCAGTGTTTGCAGAGGGAGT
AGTATTTGGTTCCTGGTCAGTTTCTGCTTTGCTTATGGTACTGCTGTCTGGAGTAATCGCTTTCATGGTGAACTTATCGA
TTTACTGGATCATTGGGAACATGTCACCAGTCACCTACAACATGTTCGGACACTTCAAGTTCTGCATCACTCTCTGCGGA
GGATACATTCTATTTAAGGATCCCCTGTCGGTAAACCAGGGACTCCGCATCCTATGCACATTCTTCGGTATCCTCACCTA
CACCCACTTTAAACTCAGTGATCAGGAAGACAGTAAG

Alignment

ORF - retro_mmus_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASLADRVRGNGRIAAGLLFNLLVSICIVFLNKWIYVHHG-FPNMSLTLVHFVVTWLGLYICQKLNIFAP
          MASLADRV.GN.RIAAGLLFNLLVSICIVFLNKWIYVHH..FP.MSLTLVH..VTWLGLYI.QKL.IFA.
Retrocopy MASLADRVWGNRRIAAGLLFNLLVSICIVFLNKWIYVHHA<FPKMSLTLVHVMVTWLGLYIYQKLDIFAL

Parental  KSLPLSKLLLLALSFCGFVVFTNLSLQNNTIGTYQLAKAMTTPVIIAIQTFWYQKRFSVRIQLTLIPITV
          K.LPLSKLLLLALSFCGFVVFT.LSLQNNTIG.YQLAKAMTTPVIIAIQTFWYQKRFS.RIQLTLIPITV
Retrocopy KNLPLSKLLLLALSFCGFVVFTKLSLQNNTIGIYQLAKAMTTPVIIAIQTFWYQKRFSIRIQLTLIPITV

Parental  GVILNSYYDVKFHSLGMVFAALGVVVTSLYQVWVGAKQHELQVNSMQLLYYQAPMSSAMLLVAVPFFEPV
          GVILNSYYD.KFHSLGMVFA.LGVVVTSL.QVWVGAKQHELQVNS.QLLYYQAP.SS.MLLVAV.FFEPV
Retrocopy GVILNSYYDLKFHSLGMVFATLGVVVTSL*QVWVGAKQHELQVNSIQLLYYQAPVSSTMLLVAVHFFEPV

Parental  FAEGGIFGPWSVSALLMVLLSGIIAFMVNLSIYWIIGNTSPVTYNMFGHFKFCITLCGGYILFKDPLSVN
          FAEG..FG.WSVSALLMVLLSG.IAFMVNLSIYWIIGN.SPVTYNMFGHFKFCITLCGGYILFKDPLSVN
Retrocopy FAEGVVFGSWSVSALLMVLLSGVIAFMVNLSIYWIIGNMSPVTYNMFGHFKFCITLCGGYILFKDPLSVN

Parental  QGLGILCTLFGILTYTHFKLSEQEGSK
          QGL.ILCT.FGILTYTHFKLS.QE.SK
Retrocopy QGLRILCTFFGILTYTHFKLSDQEDSK

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	0.14 RPM	15.89 RPM
SRP007412_cerebellum	0.04 RPM	15.63 RPM
SRP007412_heart	0.00 RPM	4.23 RPM
SRP007412_kidney	0.00 RPM	25.06 RPM
SRP007412_liver	0.00 RPM	8.77 RPM
SRP007412_testis	0.00 RPM	2.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_287 was not detected

EST

No EST(s) were mapped for retro_mmus_287 retrocopy.

TSS

No TSS is located nearby retro_mmus_287 retrocopy 5' end.

Lab

retro_mmus_287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031919	1 retrocopy	retro_btau_642,
Choloepus hoffmanni	ENSCHOG00000013347	1 retrocopy	retro_chof_2348,
Cavia porcellus	ENSCPOG00000004322	3 retrocopies	retro_cpor_1404, retro_cpor_1487, retro_cpor_339,
Homo sapiens	ENSG00000175782	1 retrocopy	retro_hsap_513,
Gorilla gorilla	ENSGGOG00000012605	1 retrocopy	retro_ggor_473,
Mus musculus	ENSMUSG00000060181	1 retrocopy	retro_mmus_287 ,
Pan troglodytes	ENSPTRG00000005201	1 retrocopy	retro_ptro_383,
Pteropus vampyrus	ENSPVAG00000002545	1 retrocopy	retro_pvam_710,