RetrogeneDB ID: retro_mmus_3028

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:57878808..57881226(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Depdc1a
• Ensembl ID: ENSMUSG00000028175
• Aliases: Depdc1a, 5830484J08Rik, Depdc1
• Description: DEP domain containing 1a [Source:MGI Symbol;Acc:MGI:1923381]

Sequence

>retro_mmus_3028
ATGGAGCGTCAGGGTGCTCCTCTTGGACCTTACCGGGCCACCAAGCTGTGGAATGAAGTAACCACATCTTTTCGAGTAGG
AATGCCTTTAAGAAAACATAGACAACATTTAAAAAAATATAGCAATTGTTTCACTGCAGTTGAAGCTATAGATTGGCTTT
ATGATCTGTTAAGAAGTAATAGTAATTTTGGTCCTGAAGTTACAAGACAACAGACTATTCAACTATTGAGAAAATTTCTT
AAGAATCATGTGATTGAAGATATCAAAGGTAGATGGGGATCAGAAAGCCTTGATGACAACAATCAACTATTCAGATTTCC
TGCAACTTCTCCACTTAAAACTTTTCCACAAAGACATACAGAAATCAAGAAAACCAACACAGAGTACTTTTCCAAAGACA
AAGATGGTATTTTTAAATTACGAAACTTATCTCAAAAAACTTCTAAGAAGCGTGGATTACATTTCTCTCAGGAAAATACA
GAAAAGATAAATCATGAAAGAATAACCAATGAAGATCTAGAAATTGCACCTGACAACCAAGAAATAAGCCAGGAAGATGT
TGAAGAAGTTTGGAGATACGTTATTATGATATACCTGCAAACCATTTTAAGTTTGCCATCCATAGAAGAACTCTTAAACC
CAAACCAAGTAATTCCTCAATATATAATGTACAACATGGCCAACACAAGTAAGCATGGAGTGGTCATACTACAAGACAAA
TCAGACGATCTTCCACATTGGGTTTTATCTGCAATGAAGTGCCTAGCAAATTGGCCAAGAAGTAATGACACCAATAATCT
AACTTATGTTGGATTTGAACGTGATGTATTCAAAACAATTGCAGATTATTTTCTAAATCTCCCTGAACCTCTACTTACAT
TTGAATATTATGAATTATTTGTGAACATTTTGGTTGTTTGTGGCTACATCACAGTTTCAGATAGAACAAGTGGAATACAT
AAAATACAAGATGATCCACGATCTTCAAAAATCCATGATTTAAGCAATTTGAATTCCTTCAAATCAACTGAGTGTCTTCT
TCTCAGTCTGCTTTACAAAGACAAAAGCAATGAAGAGTTGGATTCTACTAAAAGACTACAAAGAAATGACCAAGGATTTC
AAGAAAGATGTACCAAGAAAATGCAGCTAGATAATTTAAGAAACAGAAGAGCTAGTGCTAATGACATAATGGGAGGAAGC
TGTCATAATTTAATGGGCTTAAGTAATACAAATGCCCTGTCCTCTAACATCAAACCAAGGTGCTCTTCTTTGGAAGGAAT
TGTAGATAGGCCAGTGAATTCAAGTGAAAAGAAGTCCAGTATCTTCTACCAGTCTGTTCTGAACATAGAAGAACAAAATA
GTAAGCAATCGTTAGTGTCTGCACCCAAACAGACACCCCTATTTAATCTTCACTCAGATGAAAATGCTCAGCAGCCACAC
TGTGTTGGTTTTAACAGAACCTCTGCTTTGACTGTTCAAGACCAAGAAGAGTTATGTAATGAAAAGTATAAGTCAAAACA
GCTTTGTAGATCTCAGAGTTTACTTTTAAGAAGTAGTACAAGACAGAATAGTTGTATCAATAAACCAGTGGCTGAAATTA
TAATGAAACCAAATGTTGGACAAGGCAGTACAAGTGAGCTCGGAGAGTCTAGTACCACAATCAATAAAAGACTGTGCAAA
AGCACCATAGAACTTTCAGAGAAATCTTTACCTCCAGCTGCTTCTGTGTTGACTGGCACACAAAGTTTGCTGCAACCTCA
CTTAGAGAGGGTTGCCATCAATGCTCTACAGTTATGTTGTTTGTTACTTCCCCCACCAAATCGTAGAAAGCTTCAACTCT
TAATGCGCATGATTTCTAGAATGAGTCAAAATGTTGATATGCCCAAACTTCATGAACAAATAGGTACAAGATCATTGATG
ATAAATACTTTTTCTCGATGTGTACTATGTTGTGCTGAAGAAGTGGATCTTGATGAGCTTCTGGCTTCAAGATTAGTTTC
TTTCCTAATGGATCATCATCAGGAAATTCTTCAAGTACCCACTTATTTACAAGCTGCAGTGGAGAAACATCTTGACTACA
TTAAAAAGGGCAATGTTAAAAATCATGGAGATGGACTAGTTGTTCCTTTGCCAACATATTCTTACTGTAAACAGATTAGT
GCTAAAGAATTTGATGAACAGAAAATTTCAACTTCCCAAGCTGCAATTGCAGAACTTTTGGAGAATATTGTCAGAAGTAA
AAGCTTGCCTCTAAAGGAGAAAAGAAGAAAATTGAAACAGTTTCAGAAGGAATACCCCTTGATATATCAGAAAAGATTTC
CAACCACTGAGAGTGAAGCAGCACTTTTTGATGATAAACCTACAATCAAGTAACCGATGCTGAATTTAAGAAACCCCAAG
CTTCACAGTCTGTGTTAC

Alignment

ORF - retro_mmus_3028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERQGAPLGPYRATKLWNEVTTSFRVGMPLRKHRQHLKKYSNCFTAVEAIDWLYDLLRSNSNFGPEVTRQ
          MERQGAPLGPYRATKLWNEVTTSFRVGMPLRKHRQHLKKYSNCFTAVEAIDWLYDLLRSNSNFGPEVTRQ
Retrocopy MERQGAPLGPYRATKLWNEVTTSFRVGMPLRKHRQHLKKYSNCFTAVEAIDWLYDLLRSNSNFGPEVTRQ

Parental  QTIQLLRKFLKNHVIEDIKGRWGSESLDDNNQLFRFPATSPLKTFPQRHTEIKKTNTEYFSKDKDGIFKL
          QTIQLLRKFLKNHVIEDIKGRWGSESLDDNNQLFRFPATSPLKTFPQRHTEIKKTNTEYFSKDKDGIFKL
Retrocopy QTIQLLRKFLKNHVIEDIKGRWGSESLDDNNQLFRFPATSPLKTFPQRHTEIKKTNTEYFSKDKDGIFKL

Parental  RNLSQKTSKKRGLHFSQENTEKINHERITNEDLEIAPDNQEISQEDVEEVWRYVIMIYLQTILSLPSIEE
          RNLSQKTSKKRGLHFSQENTEKINHERITNEDLEIAPDNQEISQEDVEEVWRYVIMIYLQTILSLPSIEE
Retrocopy RNLSQKTSKKRGLHFSQENTEKINHERITNEDLEIAPDNQEISQEDVEEVWRYVIMIYLQTILSLPSIEE

Parental  LLNPNQVIPQYIMYNMANTSKHGVVILQDKSDDLPHWVLSAMKCLANWPRSNDTNNLTYVGFERDVFKTI
          LLNPNQVIPQYIMYNMANTSKHGVVILQDKSDDLPHWVLSAMKCLANWPRSNDTNNLTYVGFERDVFKTI
Retrocopy LLNPNQVIPQYIMYNMANTSKHGVVILQDKSDDLPHWVLSAMKCLANWPRSNDTNNLTYVGFERDVFKTI

Parental  ADYFLNLPEPLLTFEYYELFVNILVVCGYITVSDRTSGIHKIQDDPRSSKIHDLSNLNSFKSTECLLLSL
          ADYFLNLPEPLLTFEYYELFVNILVVCGYITVSDRTSGIHKIQDDPRSSKIHDLSNLNSFKSTECLLLSL
Retrocopy ADYFLNLPEPLLTFEYYELFVNILVVCGYITVSDRTSGIHKIQDDPRSSKIHDLSNLNSFKSTECLLLSL

Parental  LYKDKSNEELDSTKRLQRNDQGFQERCAKKMQLDNLRNRRASANDIMGGSCHNLIGLSNTNALSSNIKPR
          LYKDKSNEELDSTKRLQRNDQGFQERC.KKMQLDNLRNRRASANDIMGGSCHNL.GLSNTNALSSNIKPR
Retrocopy LYKDKSNEELDSTKRLQRNDQGFQERCTKKMQLDNLRNRRASANDIMGGSCHNLMGLSNTNALSSNIKPR

Parental  CSSLEGIVDRPVNSSEKKSSIFYQSVLNIEEQNSKQSLVSAPKQTPLFNLHSDENAQQPHCVGFNRTSAL
          CSSLEGIVDRPVNSSEKKSSIFYQSVLNIEEQNSKQSLVSAPKQTPLFNLHSDENAQQPHCVGFNRTSAL
Retrocopy CSSLEGIVDRPVNSSEKKSSIFYQSVLNIEEQNSKQSLVSAPKQTPLFNLHSDENAQQPHCVGFNRTSAL

Parental  TVQDQEELCNEKYKSKQLCRSQSLLLRSSTRQNSCINKPVAEIIMKPNVGQGSTSELGESSTTINKRLCK
          TVQDQEELCNEKYKSKQLCRSQSLLLRSSTRQNSCINKPVAEIIMKPNVGQGSTSELGESSTTINKRLCK
Retrocopy TVQDQEELCNEKYKSKQLCRSQSLLLRSSTRQNSCINKPVAEIIMKPNVGQGSTSELGESSTTINKRLCK

Parental  STIELSEKSLPPAASVLTGTQSLLQPHLERVAINALQLCCLLLPPPNRRKLQLLMRMISRMSQNVDMPKL
          STIELSEKSLPPAASVLTGTQSLLQPHLERVAINALQLCCLLLPPPNRRKLQLLMRMISRMSQNVDMPKL
Retrocopy STIELSEKSLPPAASVLTGTQSLLQPHLERVAINALQLCCLLLPPPNRRKLQLLMRMISRMSQNVDMPKL

Parental  HEQIGTRSLMINTFSRCVLCCAEEVDLDELLASRLVSFLMDHHQEILQVPTYLQAAVEKHLDYIKKGNVK
          HEQIGTRSLMINTFSRCVLCCAEEVDLDELLASRLVSFLMDHHQEILQVPTYLQAAVEKHLDYIKKGNVK
Retrocopy HEQIGTRSLMINTFSRCVLCCAEEVDLDELLASRLVSFLMDHHQEILQVPTYLQAAVEKHLDYIKKGNVK

Parental  NHGDGLVVPLPTYSYCKQISAKEFDEQKISTSQAAIAELLENIVRSKSLSLKEKRRKLKQFQKEYPLIYQ
          NHGDGLVVPLPTYSYCKQISAKEFDEQKISTSQAAIAELLENIVRSKSL.LKEKRRKLKQFQKEYPLIYQ
Retrocopy NHGDGLVVPLPTYSYCKQISAKEFDEQKISTSQAAIAELLENIVRSKSLPLKEKRRKLKQFQKEYPLIYQ

Parental  KRFPTTESEAALFDDKPTIKQPMLNLRNPKLHSLRY
          KRFPTTESEAALFDDKPTIK.PMLNLRNPKLHSL.Y
Retrocopy KRFPTTESEAALFDDKPTIK*PMLNLRNPKLHSLCY

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	0.05 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.05 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3028 was not detected

EST

No EST(s) were mapped for retro_mmus_3028 retrocopy.

TSS

No TSS is located nearby retro_mmus_3028 retrocopy 5' end.

Lab

retro_mmus_3028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3028 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013839	1 retrocopy	retro_cpor_735,
Homo sapiens	ENSG00000024526	2 retrocopies	retro_hsap_1545, retro_hsap_4206,
Gorilla gorilla	ENSGGOG00000016316	1 retrocopy	retro_ggor_1176,
Macaca mulatta	ENSMMUG00000017766	1 retrocopy	retro_mmul_1176,
Mus musculus	ENSMUSG00000028175	1 retrocopy	retro_mmus_3028 ,
Nomascus leucogenys	ENSNLEG00000009334	1 retrocopy	retro_nleu_2931,
Otolemur garnettii	ENSOGAG00000000934	1 retrocopy	retro_ogar_1907,
Pongo abelii	ENSPPYG00000001248	1 retrocopy	retro_pabe_3441,
Pan troglodytes	ENSPTRG00000000847	2 retrocopies	retro_ptro_1041, retro_ptro_2855,