RetrogeneDB ID: retro_ecab_1042

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: Un0076:71893..75229(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDLBP
• Ensembl ID: ENSECAG00000012829
• Aliases: None
• Description: high density lipoprotein binding protein [Source:HGNC Symbol;Acc:4857]

Sequence

>retro_ecab_1042
TCCAAAGAAAATTTGACTGAGCACCAAAGTAGGTCCATTCAAAAAGGCAATTATGTTACTGCTTTAAATTCAGAAGAACA
TATTGGCACTCCAACCTACAAAGGTAAATTCAGTCAACTCTTAGAGAAAAGAAATTGGTTGGAAAATGCTCAGGAACCTG
CTGAATGCTTGAGTAACAATAGTCAGCCTAGCACAACCTCAGTCATCACTCAAGTCTTTCATGTGCCTCTAGAGGAGAAC
GAGTATGTGAATCAGTTTGGTAAAGATAGACAAGGAAAATTCTACCTAGATATCATGCAAAAGACTGGTGCCAATGTAGA
ATTAATTTTTGTCAAAGACCAGGGCCTCTACATTATAGTCTCTGGTGAAACAGAAACTGTCATGAAAGCTCAGAAGGAGA
TTTTTACATGGTTTCAGGATCGAGGTTTAACTGCAGTGTCCATTCCCGAAGAACAGCCGTGCTTTGTTACAGGCAAGACT
GGAGGAGAAATGCAAGACTTAGAAGAAAAAGATGCAACCTACATCCAGAACTTATGCCCAGATAACCACAGCAACTGGAT
TAATACTGTGGGCATCAAAGAGGTCATGAAGAAGGATTTACATGAAGTCCTAGGTATGTCTACTGATCAAGACAAATGTG
CTGTAGAGAAGTTAGATGAGAAAAAAGCATTTTTTCCTTCCACTCCTGGACCATCCAGTAAAACTTTTGACAAAATTATA
CCAGAAACAGAGGCACACATCCATGTTCCACCACCTAGTGTCGATCAGACACAAGTAGGCTTTACTGAAAAAAAGCAGCA
GCTTAATGAGGCTCAGGCTTGTGTAAAGGAGATTTTTGACAGCACTAAAAAGAAAAACACACCCATCAATGCAGAGATGA
AATTTCAGCACAAGTGTACCATAGGTCCCAAGAGAAATTCTGTGCAGGAGACCTTGCCAAGAAGTGGAATTTCAATAGAG
ATCTTACCCGTAGAGAGCATGTCAGCTTCTGTGACAGAGCAAGGTGAGCCTGGAAGCTCAGGGAAGGCATTTTCCAAAGC
CAGTTCGAAGACCGAACGTTACACTGTTTCCTCGATCTTTGTACCTTCCTGGCTTCACAGATTTATTATTGGTAAGAAAG
GTTGTAATATATCTGAAATCACACACAGCATGCCAAAAGTTCACATAGAATTTACTGAAGGAGATAAAATTACAATAAAA
GGACCAAAAGAAGATGTGAATGATGCTCAAGAACAAATTGAGGTCATAGTCAAAGATCTAATTAACAGGATGGATTATGC
AGAAATCAATGTTGACTGTAAGTTTCACAAACATCTGATAGGGAAGAATGATGCCATCATAAAGCAAATTAAAGAGAGGA
ATAATGTTTCTGTGCTAATGTCACCTAAAAATGTAAAGAATAAATTGATTAGAATTGAGGGGGAATCTCAGGGAGTCCAA
CAAGCCAAGAGAGAACTTCTTGAACTTGCTGGTCATTTAGAAAATGAGCACAGCAAGGATTTAATCATTGAGCAAAGATT
TCACCCTGCAATCATTGGGTGGAAAGGTGAACGGATCCATGACATCCAGAAGAAATTCCCAGAGGTGATGATTCATTTTC
CTGACCAAGCACAAAAAAGTGACACAGTCCAACTTAGAGGGCCAAAACATGAAATAGAAAAATGCACACAATATTTGGAG
AATGTGGTGGCAGACATTGTAGAGAGTAGCTATTCCGTAACTATTCCCAACTTTAAAAAGCCTCACAGAAATGTCAATGG
AGAAGGAGGTGCAAACATAAAAAAAATCTGTGCAGCAAGCAACACCAAAAGTAATCCTCCGTCGGCAAGTGGCTACTCAG
AAGATATTGTCATCAGTGGAAAACCTGCAAACTGTGAAGTAGCTTCTAACTGGATTCTTCCAACTCAGAAACATATAACC
AATAGTTCAGAGGTAGAAATTTCTATTCCTTCCAATCTATACAAGTCTCTTACCGATTCTAAAGACTGTTTGATTGGTGC
AATCATGCAAGAATGTGGAAGGATCCACATCCACTTTCCAAAAATGGACTCAGGCCTTCAAAGAGTCATTATTAGGGGCC
CTGCCCAAAGTGTTGAAAAGGCCAAGACAAAACTGCTACAACTAGCAGAAGAAGAGCAAACCAAGAGTCATACTGTAATT
CTCCACGTCAAACCACAGTATCACAAATTCCTCATGAATAAAAATGGTGGCAATGTTTCCAAAGTCTGTAATGAGACTGG
AGCGCACATCATTTTCCCTATCCCTGAGGACAAGGATCAAGAATTGTTAACTATTAAAGGAACAGAGAAGGCTGTCAAAG
ATGCACAAAAGGGACTAGCGGCACTAATTACAAATCTAGATAACATTGTAGAGGAGGACATACTGATAAATCCTGTTTAC
CACCATCATTTTTTCATGAGAAGAGGCCCGGTTTTTCGCGAGATAACTGAGGAGTATGGTGGTGTTAGTATTAACTTTTC
ATATTCAGGAAAACAGAGAAGCAAAGTCACAATCAAAGGAGCAAAGCCTTGTGTGGAAGCCGCCAAAAAGCACATTCAGG
AGATTACTGGGGACTTGGATAGTCAAGTCACAACAGAATGTATTATTCCCCAGAAGTTCCATCATTTTATCATGGGACAA
ATGTGTTCTCGAATCCAACAAATTACTAGAGATTATAATGTCCAAATCAAATTCCCAGATAAAGAGAACTCAGTTACTAA
TATGGATCCAACCATTCAGAAAAATGAGGAAGAAGTTAGGGAAAAGAGCACTACGGAAGCTGCTTCTATTTCCCCAAGGA
AATGTGACACCATACTTATCTCTGGCCAAAAGGAAGAGTGTGCAGCAGCCATGGAAGCCCTTGAGGCTTTAATTCCTGTC
ACTGCTGAACTAGACGTGCCCTTTGACCTACACCATTATATCATTGGTCAGAAAAGAAGAGAGATACGAAAGATAATGGA
TAGGTTTGAAGTTAATATACACATGTCAACACCTGGATTGGCATCTGATATCCTTTTTATCACGGGCCTTGCTGCAAATG
TGGAGCAAGCCAAAGCTAGGTTACAAGAACTTGTCAAGGCTTTACAAAACGAAGCAAAAGATCGAGCATTAAGAAATTTT
AAACTCAAGTTCACAGTAGACCCCAAATATCACCCTAAGATCATTGGTCACAAAGGGGTAGTTATTACTCAGATTTGCTT
GAAGCATAAGGTTGCTATTCATTTTCCACGTAAAGGAAGTGATGAGACACAAGACCAAATCACCATCACTGGATATGAAA
ATAACACCATCGCTGCCCAGAATGCAATCATGAAACTGGTGCATAAATTTGAAAAA

Alignment

ORF - retro_ecab_1042 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.53 %
• Parental protein coverage: 88.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TQESFAEHRSGLVPQQIKVATLNSEEESDPPTYKDAFPPLPEKAACLENAQEPAGAWSNKIRPIKASVIT
          ..E...EH.S........V..LNSEE....PTYK..F..L.EK...LENAQEPA...SN...P...SVIT
Retrocopy SKENLTEHQSRSIQKGNYVTALNSEEHIGTPTYKGKFSQLLEKRNWLENAQEPAECLSNNSQPSTTSVIT

Parental  QVFHVPLEERKYKDMNQFGEGEQAKICLEIMQRTGAHLELSLAKDQGLSIMVSGKLDAVMKARKDIVARL
          QVFHVPLEE..Y...NQFG...Q.K..L.IMQ.TGA..EL...KDQGL.I.VSG....VMKA.K.I....
Retrocopy QVFHVPLEENEY--VNQFGKDRQGKFYLDIMQKTGANVELIFVKDQGLYIIVSGETETVMKAQKEIFTWF

Parental  QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDASNQIRITGTKEGIEKARHEVLLISA
          Q......V.IP.E...FV.GK.G...QDLE.K.AT.IQ...PD..SN.I...G.KE...K..HEVL..S.
Retrocopy QDRGLTAVSIPEEQPCFVTGKTGGEMQDLEEKDATYIQNLCPDNHSNWINTVGIKEVMKKDLHEVLGMST

Parental  EQDKRAVERLEVEKAFHPFIAGPYNRLVGEIMQETGTRINIPPPSVNRTEIVFTGEKEQLAQAVARIKKI
          .QDK.AVE.L...KAF.P...GP.......I..ET...I..PPPSV..T...FT..K.QL..A.A..K.I
Retrocopy DQDKCAVEKLDEKKAFFPSTPGPSSKTFDKIIPETEAHIHVPPPSVDQTQVGFTEKKQQLNEAQACVKEI

Parental  YEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSVEIPPSDSISETVILRGEPEKLGQALTEV
          ....KKK.T.I..E.K..QHK..IGPK.NS.QE.L.R.G.S.EI.P..S.S..V...GEP...G.A....
Retrocopy FDSTKKKNTPINAEMK-FQHKCTIGPKRNSVQETLPRSGISIEILPVESMSASVTEQGEPGSSGKAFSKA

Parental  YAKANSFTVSSVSAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDRITLEGPTEDVNVAQEQIEAM
          ..K....TVSS...PSWLHRFIIGKKG.N...IT..MPKVHIEFTEG.D.IT..GP.EDVN.AQEQIE..
Retrocopy SSKTERYTVSSIFVPSWLHRFIIGKKGCNISEITHSMPKVHIEFTEG-DKITIKGPKEDVNDAQEQIEVI

Parental  VKDLINRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKREL
          VKDLINRMDY.EIN.D.KFH.HLIGK..A.I..IK....VSV...P...K..LIRIEG..QGVQQAKREL
Retrocopy VKDLINRMDYAEINVDCKFHKHLIGKNDAIIKQIKERNNVSVLMSPKNVKNKLIRIEGESQGVQQAKREL

Parental  LELASRMENERTKDLIIEQRFHRTIIGQKGERIREIRDKFPEVIINFPDPAQKSDIVQLRGPKNEVEKCT
          LELA...ENE..KDLIIEQRFH..IIG.KGERI..I..KFPEV.I.FPD.AQKSD.VQLRGPK.E.EKCT
Retrocopy LELAGHLENEHSKDLIIEQRFHPAIIGWKGERIHDIQKKFPEVMIHFPDQAQKSDTVQLRGPKHEIEKCT

Parental  KYMQKMVADLVENSYSISVPIFKQFHKNIIGKGGANIKKIREESNTKIDLPAENSNSETIIITGKRANCE
          .Y....VAD.VE.SYS...P.FK..H.N..G.GGANIKKI...SNTK...P.....SE.I.I.GK.ANCE
Retrocopy QYLENVVADIVESSYSVTIPNFKKPHRNVNGEGGANIKKICAASNTKSNPPSASGYSEDIVISGKPANCE

Parental  AARSRILSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSS
          .A...IL..QK...N..EVE.SIP..L..SL...K..LI..IM.ECG..HIHFP...SG...V.IRGP..
Retrocopy VASNWILPTQKHITNSSEVEISIPSNLYKSLTDSKDCLIGAIMQECGRIHIHFPKMDSGLQRVIIRGPAQ

Parental  DVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDNTGARIIFPAAEDKDQELITII
          .VEKAK..LL.LAEE.QTKS.TV....KP.YHKFL..K.GG...KV...TGA.IIFP..EDKDQEL.TI.
Retrocopy SVEKAKTKLLQLAEEEQTKSHTVILHVKPQYHKFLMNKNGGNVSKVCNETGAHIIFPIPEDKDQELLTIK

Parental  GKEDAVREAQKELEALIQNLDNVVEDSMLVDPKHHRHFVIRRGQVLREIAEEYGGVMVSFPRSGTQSDKV
          G.E.AV..AQK.L.ALI.NLDN.VE...L..P..H.HF..RRG.V.REI.EEYGGV...F..SG.Q..KV
Retrocopy GTEKAVKDAQKGLAALITNLDNIVEEDILINPVYHHHFFMRRGPVFREITEEYGGVSINFSYSGKQRSKV

Parental  TLKGAKDCVEAAKKRIQEIIEDLEAQVTIECAIPQKFHRSVMGPKGSRIQQITRDYNVQIKFPDREENPV
          T.KGAK.CVEAAKK.IQEI..DL..QVT.EC.IPQKFH...MG...SRIQQITRDYNVQIKFPD..EN.V
Retrocopy TIKGAKPCVEAAKKHIQEITGDLDSQVTTECIIPQKFHHFIMGQMCSRIQQITRDYNVQIKFPDK-ENSV

Parental  HSVEPAVQENGDDAGEGRDAKEADPGSPRRCDIITISGRKEKCEAAKEALEALVPVTIEVEVPFDLHRYI
          ....P..Q.N.....E.....EA...SPR.CD.I.ISG.KE.C.AA.EALEAL.PVT.E..VPFDLH.YI
Retrocopy TNMDPTIQKNEEEVRE-KSTTEAASISPRKCDTILISGQKEECAAAMEALEALIPVTAELDVPFDLHHYI

Parental  IGQRGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQAEQEDRALRSFKLSV
          IGQ....IRK.MD.FEVNIH...P.L.SDI..ITGLAAN...AKA.L.E.VK.LQ.E..DRALR.FKL..
Retrocopy IGQKRREIRKIMDRFEVNIHMSTPGLASDILFITGLAANVEQAKARLQELVKALQNEAKDRALRNFKLKF

Parental  TVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILKIVGELEQ
          TVDPKYHPKIIG.KG.VITQI.L.H.V.I.FP.K......QDQITITGYE.NT.AA..AI.K.V...E.
Retrocopy TVDPKYHPKIIGHKGVVITQICLKHKVAIHFPRK-GSDETQDQITITGYENNTIAAQNAIMKLVHKFEK

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
SRP021940_articular_cartilage	0.00 RPM	596.08 RPM
SRP021940_cerebellum	0.00 RPM	184.52 RPM
SRP021940_embryo	0.00 RPM	443.66 RPM
SRP021940_placental_villous	0.10 RPM	300.89 RPM
SRP021940_synovial_membrane	0.00 RPM	570.26 RPM
SRP021940_testis	6.65 RPM	880.24 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1042 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1042 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1042 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,