RetrogeneDB ID: retro_mmus_194

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:127060193..127063946(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000062791
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Hdlbp
• Ensembl ID: ENSMUSG00000034088
• Aliases: Hdlbp, 1110005P14Rik, AA960365, AI118566, D1Ertd101e
• Description: high density lipoprotein (HDL) binding protein [Source:MGI Symbol;Acc:MGI:99256]

Sequence

>retro_mmus_194
ATGAATTCCAAAAGAAATTCTGCTTCACAACAAAACAAGTCTGCTCAAAAAGAAAATCATTATAAAAATCCAAATGATGT
GGTTCGTATGTCCAGAAATGACAAGGAAGTCAATCAACACCTAGAGCAAGGAAACTTTTCAGGAAATCCTGAAGAAACTG
CAGAATCATCAAACAGTAATATTTTTAAGGCTGGGGAAATTTCAAACCTTACTCGGATTTTTCATGTATTACTAGAAGAA
GAAAAGTATTTGACTCAATTTGGAGAAGGTACATTAGCAAAGTTCTATGCACATATCATGGAAAACACTGGTGTCAACTT
AGAATCATCTTTTGTCAAAGACCAAGGTCTTTATGTGACAGTTTTTGGCAACCCAGAAGCTGTCACAAATGCTGAGAATG
AAATTTTTAAATGGTGTCAAAAACAATATTTACCTTTAACTCTCATTTCCAAACAAGAACATTGTTTTTTTCTAAACCAG
ACTGGTAATAAATCACAAGATTTGGAGCAAGAAGGTCAAATAAACACTCAGATCACAAGTCCACATAATCAGAACAACAG
TATAAATAGTGTTGATGTGAATCAGACAAAGATGAAGTCTTCAGATGGAAGCCTATCTACATCTGCCAGAAGTAACAAAG
GTGATATCCAGATACTAGAAATGGAGAAATCATTTAATCCCCTGACTGTGAAGCCATACCTTCAAGCAAGTGACATTTTC
CAAGAAACAGAGGAGCATGTCCCTTTTGAACTCTCTAGTGCCAAGGAGACAGATTTAGATATTAATGAAGGACAACTGCA
TGTGGATCAGATAGGTTGTCTTAAAAATGATATGATTAAAAAAACCAGTACTATAACTGAGGGTATGATGATGACATTTC
AAGACAGTGGTACCAGAAGTCTCAAAAGACATTTTCTAGAAGAGATCCTAGACACAAGTGAAGATTCAACAGGACAGTCA
CAATCAGAAAGCATATCAGATTATATGACACAACACAGTGATCTTGACAGTTCTGGGGAATTATTTAATGAAGCCGATGA
CAATGATGATGACTACATTGCTTCTTCAATCTTCGCTCCTTCTTGGTTGCACAGGTTTATTATTGGTACAAAAGGTGAGG
AAATATCTGAGATAACAGAGTGTGTGCCAAAGGTTCAAATACATTTTACAGCTAAAGACAAGATAACACTGAAGGGACCA
ATAGATGACGTAAATTATGCTCAAGAAAAATTTGACATCATTGTCAAGGACCTAATGAGTAAAATGGAATATACTGAGAT
AAACAGTGACAGTAAATTTTACAAATACCTGACAGGAAATAATGGGGAGATTCTAAATAGAATTACAGAGAAGAACCAAG
TCTCTATCACAATGTTTCCTGAAAATGAGTCGAACTACTCAATCAGAATTGAGGGAGAATCTCTGGGTGTCCACCAGGCC
AAAAAAGAACTACTTGATCTGGCAAATAACTTGGAAGAAGAGTATAGCCAGGACATAATCATCAAACACCAATTTCATCA
CATTCTTATTGGCCAAAAAGGTGAAAGAGTTCGAGAAATTTGTAAGAAATTCCCTGATGTTATCCTCAACTTTCCACACC
CTGCAGAGAAAAGTGATATTGTTCAACTGATAGGGCCAAGATATGAATCAGAAAAGTGTGCACAGTATTTAGAGAATATG
TTGACAGATATTAAAGAAAATAACTATTCTATAAGTGTTCCTATAATAAAAAAGCTTCACAAAAGGATAATTGGAAAAGG
AGTTTCAAACATTAGAAAAATCTCTGAAGCAACCAATACCAAAATTACTTTTCCACCAGAAAGCTGCAATTCAGAAGAGT
TCATCATTACTGGATATCCAGAAAATTGTGAAATTGCACGTAACTGGATACTTTCACTTCAGCAAGAGTTAGCTGATACT
GCAGAGGAGGAAATTATCATTCCTGCTAATCTATACAAACATCTGACTAATCCTAAAGAATGTTTGTTAAATTCAATCAT
AGAAGAATGTGGGAAGATCCATCTGCATTTTCCAAAAGGCAAATCAAACCTGAATAAAATCATTATCATGGGCACCATCG
AAAATGTTGAAAAGGCCAAAACAAAACTTCTAAAACTTTCAGAAGAAGAACAAGCCAAAAATTACTCTGAGACTCTTCAT
ATCAAATCAAAGTACCATCAATTCCTACTGAACAAAAATGGAGGTAATATTTCCAAAATCTGTGATGAGACTGGGACATG
TGTCTTTTTCCCTAACCCTACAAATAAGGATCAAGAAACCATAACAATTACAGGGACTGAGGAGTCTGTTAAAGAGGTCC
AAAAACAACTAGATGATTTAGTTAAAGACTTTGAGAATGAGGTGGATGATTCCATACTAATAAACCGTAGATTTCACCAT
TATTTTGTCATGCGGAGAGGCCAGCTTTTAAAAGAAATGGCAGAAGACTATGGTGGTGTAGTTATTACATTCTCTTATTC
AGGGAGACAGAATACAAAAGTCACAATAAGAGGGGCAAAACCTTGTGTTGAGGCAGCAAAGAAACACATTAAGGAGATTT
TTGAGCCTTTGGGCTCCCAAATTACAACTCGGTATGTTCTACCCCACTCTTTCCAACCTTTTATCATGGGACCAATAAGT
TCGAGAATCCAACAAATTGCTAGGGATTATAAAGTTGAAATCAAATTTCCAGATATAGAGAAGCCAGCCTTAAATATGGA
TTTAGGTACTCATGAGAAAGGAAAAGAAAAGTGGAAAAGGACTGCTAAAGAGATTGCTCCCAATTCCCCAAGGAAAGGTG
ACACCATATTTATCTCAGGTCAAGTGGAAAATTGCAAGGCAGCTACTGAAGCTCTAGCATCTATAATTCCTGTTACTACT
GAAGTCCATGTGCCCCTTCACCTACAACCTTACATCATTGGGCACAAGGGAAGTGGTTTACGCAAACTAGTAAAGGAATA
TGAAGTGCATATGCAGGTGTCACAACCTGGAAAAAATTCTGATATAATATCTATTATGGGTCTTTCAGCAAATGTGGAAC
AAGCCAAGATAAAATTACAAAAGCGAGTCAAGTCTTTACAAATGGAAGTAGAAGATCGAACACTAAGAAATTTTAAGTTA
ATGTTTAATCTAGATCCTAAATATCAAGCCAAGATCACCGGTCACAAGGGCTTGCTTATTACTCAAATTTGCACAGAACA
TGATGTTACTATCCATTTTCCAAAGAAAGGAACCCATGATATGCAAGAACAAATCACTATTACTGGTTATAAAGAGAACA
CCCTAGCTGCCCGAGATGCAATAATGAGATTGTTGCATAAAATTGAAAAAACAATTTCTAAGGAAATCACCCTAAACCAG
CAGGTTCGTGGCAATGTTATTGGAGTACGTGGAAAAACCATCAATAAAATCATGGATCAATACCAAGTAGATATACGTTT
ACCTCCAAAAGGGTTATATAATCCTAATATCACAGTGACTGGTCTCGCTGATAATGTAGAAAAAGCAATTGAGCATATTC
TTAATCTTGAAAAGTATTATCTATCAGCTGCCATAAACCACGGATCTCAGCAAGAACAACCTAAAAGTATGTCCCTTTGC
AATATAGCCATGACACCATCCAAGAGTTTTGTGAGAAAGTATGTTCCCTGTTATGCTAAAACAACCACAAAGCTCCCAGA
TGTAGATAATTGTGAACACTTTCCAAGATTAAAACAGCGAACATCTTCTAAAACTCATCCTTCAAAATTGTGA

Alignment

ORF - retro_mmus_194 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.5 %
• Parental protein coverage: 70.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGNSLQEILERTGVSVEIPPSDSISETVILRGEPEKLGQALTEVYAKANSFTVSSVSAPSWLHRFIIGKK
          K...L.EIL.....S.....S.SIS............G....E..........SS..APSWLHRFIIG.K
Retrocopy KRHFLEEILDTSEDSTGQSQSESISDYMTQHSDLDSSGELFNEADDNDDDYIASSIFAPSWLHRFIIGTK

Parental  GQNLAKITQQMPKVHIEFTEGEDKITLEGPTEDVNVAQEQIEGMVKDLINRMDYVEINIDHKFHRHLIGK
          G.....IT...PKV.I.FT...DKITL.GP..DVN.AQE.....VKDL...M.Y.EIN.D.KF...L.G.
Retrocopy GEEISEITECVPKVQIHFT-AKDKITLKGPIDDVNYAQEKFDIIVKDLMSKMEYTEINSDSKFYKYLTGN

Parental  SGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLELASRMENERTKDLIIEQRFHRTII
          .G...NRI.....VS....P..E....IRIEG...GV.QAK.ELL.LA...E.E...D.II...FH...I
Retrocopy NGEILNRITEKNQVSITMFPENESNYSIRIEGESLGVHQAKKELLDLANNLEEEYSQDIIIKHQFHHILI

Parental  GQKGERIREIRDKFPEVIINFPDPAQKSDIVQLRGPKNEVEKCTKYMQKMVADLVENSYSISVPIFKQFH
          GQKGER.REI..KFP.VI.NFP.PA.KSDIVQL.GP..E.EKC..Y...M..D..EN.YSISVPI.K..H
Retrocopy GQKGERVREICKKFPDVILNFPHPAEKSDIVQLIGPRYESEKCAQYLENMLTDIKENNYSISVPIIKKLH

Parental  KNIIGKGGANIKKIREESNTKIDLPAENSNSETIIITGKRANCEAARSRILSIQKDLANIAEVEVSIPAK
          K.IIGKG..NI.KI.E..NTKI..P.E..NSE..IITG...NCE.AR..ILS.Q..LA..AE.E..IPA.
Retrocopy KRIIGKGVSNIRKISEATNTKITFPPESCNSEEFIITGYPENCEIARNWILSLQQELADTAEEEIIIPAN

Parental  LHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIR
          L...L...K..L..SI.EECG..H.HFP...S......I.G....VEKAK..LL.L.EE.Q.K.......
Retrocopy LYKHLTNPKECLLNSIIEECGKIHLHFPKGKSNLNKIIIMGTIENVEKAKTKLLKLSEEEQAKNYSETLH

Parental  AKPEYHKFLIGKGGGKIRKVRDSTGARIIFPAAEDKDQDLITIIGKEDAVREAQKELEALIQNLENVVED
          .K..YH.FL..K.GG.I.K..D.TG....FP....KDQ..ITI.G.E..V.E.QK.L..L....EN.V.D
Retrocopy IKSKYHQFLLNKNGGNISKICDETGTCVFFPNPTNKDQETITITGTEESVKEVQKQLDDLVKDFENEVDD

Parental  YMLVDPKHHRHFVIRRGQVLREIAEEYGGVMVSFPRSGTQSDKVTLKGAKDCVEAAKKRIQEIIEDLEAQ
          ..L.....H..FV.RRGQ.L.E.AE.YGGV...F..SG.Q..KVT..GAK.CVEAAKK.I.EI.E.L..Q
Retrocopy SILINRRFHHYFVMRRGQLLKEMAEDYGGVVITFSYSGRQNTKVTIRGAKPCVEAAKKHIKEIFEPLGSQ

Parental  VTVECAIPQKFHRSVMGPKGSRIQQITRDYNVQIKFPDREENPVHSVEPSIQENGDEAGEGREAKETDPG
          .T.....P..F....MGP..SRIQQI.RDY.V.IKFPD.E..P.........E.G.E....R.AKE..P.
Retrocopy ITTRYVLPHSFQPFIMGPISSRIQQIARDYKVEIKFPDIEK-PALNMDLGTHEKGKEKWK-RTAKEIAPN

Parental  SPRRCDIIIISGRKEKCEAAKEALEALVPVTIEVEVPFDLHRYIIGQKGSGIRKMMDEFEVNIHVPAPEL
          SPR..D.I.ISG..E.C.AA.EAL....PVT.EV.VP..L..YIIG.KGSG.RK...E.EV...V..P..
Retrocopy SPRKGDTIFISGQVENCKAATEALASIIPVTTEVHVPLHLQPYIIGHKGSGLRKLVKEYEVHMQVSQPGK

Parental  QSDTIAITGLAANLDRAKAGLLDRVKELQAEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHE
          .SD.I.I.GL.AN...AK..L..RVK.LQ.E.EDR.LR.FKL....DPKY..KI.G.KG..ITQI..EH.
Retrocopy NSDIISIMGLSANVEQAKIKLQKRVKSLQMEVEDRTLRNFKLMFNLDPKYQAKITGHKGLLITQICTEHD

Parental  VNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILKIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKI
          V.I.FP.K......Q.QITITGY..NT.AARDAI.......E...S....L...V....IG.RGK.I.KI
Retrocopy VTIHFPKKGT-HDMQEQITITGYKENTLAARDAIMRLLHKIEKTISKEITLNQQVRGNVIGVRGKTINKI

Parental  MDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEYLADVVDSEALQ
          MD...VDIR.P..G...PN..TVTGL..NVE.AI.HILNLE..YL.........Q
Retrocopy MDQYQVDIRLPPKGLYNPN-ITVTGLADNVEKAIEHILNLEKYYLSAAINHGSQQ

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	199.66 RPM
SRP007412_cerebellum	0.00 RPM	224.62 RPM
SRP007412_heart	0.00 RPM	728.04 RPM
SRP007412_kidney	0.00 RPM	524.98 RPM
SRP007412_liver	0.00 RPM	600.40 RPM
SRP007412_testis	10.61 RPM	630.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_194 was not detected

EST

No EST(s) were mapped for retro_mmus_194 retrocopy.

TSS

No TSS is located nearby retro_mmus_194 retrocopy 5' end.

Lab

retro_mmus_194 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_194 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
Equus caballus	ENSECAG00000012829	1 retrocopy	retro_ecab_1042,
Loxodonta africana	ENSLAFG00000014826	1 retrocopy	retro_lafr_1146,
Mus musculus	ENSMUSG00000034088	1 retrocopy	retro_mmus_194 ,
Nomascus leucogenys	ENSNLEG00000013818	1 retrocopy	retro_nleu_1292,
Pongo abelii	ENSPPYG00000013351	1 retrocopy	retro_pabe_1544,