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 summary: | ||
| 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] |
Retrocopy-Parental alignment summary:
>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
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 |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
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 |
RNA Polymerase II activity near the 5' end of retro_mmus_194 was not detected
No EST(s) were mapped for retro_mmus_194 retrocopy.
No TSS is located nearby retro_mmus_194 retrocopy 5' end.
retro_mmus_194 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_194 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000012829 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000014826 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000034088 | 1 retrocopy |
retro_mmus_194 ,
|
| Nomascus leucogenys | ENSNLEG00000013818 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000013351 | 1 retrocopy |