RetrogeneDB ID: retro_ecab_65

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:28168490..28171001(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004795
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000016242
• Aliases: None
• Description: Tuftelin-interacting protein 11 [Source:UniProtKB/TrEMBL;Acc:F6TXE8]

Sequence

>retro_ecab_65
ATGTCGCTGCCCCACTTTTACCGGGACGGGGAAGGCCACATGGATGATGATGAGGACGAGCGGGAGAACTTCGAGATCAC
CGACTGGGATCTCCAGAATGAATTCAACCCCAACCGGCAGCGCCACTGGCGGACCAAGGAAGAGGCCACCAATGGAGTGT
GGACAGAGCGAGCCTCGGATGGAGAGAGACCCAGCTTTGGAGGCAAACGAGCTCGCGACTGCTCAGCGCCAGTCAGCTTC
ATCAGCGCGGGGCTCAAGAAGCGGGCAGCAGAGGAGGCGGAGCTGGAAGATTCTGATGACGAAGAGGAGCCTGTCAAGCA
GGATGACTTTCCTAAGGATTTTGGACCCAAGAAGTTAAAAACGGGAGGCAACTTTACACCCAGCCAGAAAGGCTTTGCTG
GAGGAACCAAGTCTTTCATGGATTTTGGCAGCTGGGAGAGACACACAAAAGGAATTGGACAGAAGCTTCTTCAGAAAATG
GGCTACGTCCCTGGGAGGGGCCTCGGGAAGAATGCACAAGGTATCATTAAGCCAATCGAAGCCAAACAGAGAAAGGGCAG
AGGCGCTGTGGGAGCTTACGGCTCCGAGCGCACCCCCCAGTCCCTGCAGGACTTCCCTGTGGTCCACTCAAAGGAAGAGG
CCGAGGAGTTTCAGAAGGAGCTGAGCCAGTGGAGACAAGGCCCCAGTGGAAGCAAGAAGAAGCCCAAATACTTTTACAAG
ACCGTGGAAGAGTTGAAGGCCAAGGGCAGGGTTAGCAAGCAGCTCACCGCCCCCGAGAAGGAGCTTTCTCAGGTCAAGGT
CATAGACATGACTGGCCGCGAGCAGAAGGTCTACTTCAGCTACAGCCAGATCAGCCACAAGCACAACGTCCCCGGCGACG
GGCTGCTGCTGCAGTCGCCGCAGCCACCACAGCCCGGCAAAGAGGCCAAGGCCCCGGGCTTCGCGCTGCCAGAGCTGGAG
CACAACCTGCAGTTGCTCATCGACCTCACGGAGCAGGAGATCATCCAGAACGACCGGCAGCTGCAGTACGAGCGGGACAT
GGTGGTCAACCTCTCCCACGAGCTGGAGAAGATGTCGGAGGTCCTGGACCACGAGGAGCGGCTCATCTCCAAACTCAGCA
AGGTCTTGGAGATGGTGGAGGAGTGCGAGCGGTGCATGCAGCCCAACTGCAGCGACCCCCTCACGCTGGACGGGTGCACC
CACATCTTTGAGACCCTGAGGGACAAGTACTATGAGGACTACTGGATGTCCCACCGTGTGGACCTCACTGTGGCCATCGT
CTACCCACTCATGAAGGAGTACTTCAAGGAGTGGGACCCCCTCAAAGACTGTACTTATGGCACCGAGATCATCTCTAAGT
GGAAAAGCCTCCTGGAGAACGACCAGCTCCTGTCGCACGGTGAGCAGGACCTCTTGGCAGATGCCTTTCACAGGCTCATT
TGGGAAGTCTGGATGCCTCTCGTTCGAAACATTGTCACCCAGTGGCAACCAAGGAACTGTGACCCGATGGTGGACTTTTT
GGATAGCTGGGTGCACATTATCCCCGTGTGGATCTTAGATACCATCCTGGACCAGCTCATCTTCCCCAAGCTGCAGAAGG
AGGTGGAGAACTGGAACCCACTGACGGACACCATCCCCATCCATTCCTGGATCCACCCGTGGCTGCCCCTCATGCAGGCA
CGTCTGGAGCGGCTCTATTCCTCCATCCGCAGCAAACTGTCCCGTGCCCTGCAGAAGTGGCACCCCAGCGACTCCTCAGC
CAAGCTCATTCTGCAGCCCTGGAAGGAGGTCTTCACCCCTGGCTCCTGGGAAGCATTCATGGTCAAGAACATAGTGCCCA
AGCTGGAGATGTGTCTTGGCGAGTTGGTCATTAACCCCCACCAGCAGCACATGGATGCCTTTTATTGGGTCATCACCTGG
GAAGGGATGATCTCTGTCTCCAGCCTGGTGGGGCTTCTTGAAAAGCACTTCTTTCCCAAGTGGCTTCAGGTGCTGTGCTC
CTGGCTCAGTAACAGCCCCAATTATGAGGCGATCACCAAGTGGTACCTGGGTTGGAAGTCCGTGTTCTCAGACCAAGTGC
TGGCACACCTGTCCGTCAACGACAAGTTTAATGAAGCACTTGACATTATGAACAGGGCGGTGTCCTCCAATGTGGGGGCC
TACATGCAGCCCGGAGCACGAGAGAACATTGCCTACCTCACCCACGTAGAGCGGAGGAAGGACTTCCAGTACGAGGCCAT
GCAGGAGCGACGGGAGGCTGAGAACATGGCCCAGAGGGGCATTGGCATGGCCGCCGGCTCCATGCCCATGAACTTTAAGG
ACCTCATTGAGACCAAGGCTGAGGAACACAACATCGTCTTCATGCCCATCATCGGGAAGCGACACGAAGGGAAGCAGCTC
TACACCTTTGGCCCCATCGTCATGTACATTGACCGGGGAGTGGTCTTCATCCAGGGCAAGAAGACCTGGGTGCCCACCTC
CCTGCAGAGCCTGATTGACATGGCCAAGTAG

Alignment

ORF - retro_ecab_65 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLSHLYRDGEGRMDDDDDERENFEITDWDLQNEFNPNRQRHWQTKEEATYGVWAERDSDEERPSFGGKR
          MSL.H.YRDGEG.MDDD.DERENFEITDWDLQNEFNPNRQRHW.TKEEAT.GVW.ER.SD.ERPSFGGKR
Retrocopy MSLPHFYRDGEGHMDDDEDERENFEITDWDLQNEFNPNRQRHWRTKEEATNGVWTERASDGERPSFGGKR

Parental  ARDYSAPVNFISAGLKKGAAEEAELEDSDDEEKPVKQDDFPKDYGPKKLKTGGNFKPSQKGFAGGTKSFM
          ARD.SAPV.FISAGLKK.AAEEAELEDSDDEE.PVKQDDFPKD.GPKKLKTGGNF.PSQKGFAGGTKSFM
Retrocopy ARDCSAPVSFISAGLKKRAAEEAELEDSDDEEEPVKQDDFPKDFGPKKLKTGGNFTPSQKGFAGGTKSFM

Parental  DFGSWERHTKGIGHKLLQKMGYVPGRGLGKNAQGIINPIEAKQRKGKGAVGAYGSERTPQALQDFPVVDS
          DFGSWERHTKGIG.KLLQKMGYVPGRGLGKNAQGII.PIEAKQRKG.GAVGAYGSERTPQ.LQDFPVV.S
Retrocopy DFGSWERHTKGIGQKLLQKMGYVPGRGLGKNAQGIIKPIEAKQRKGRGAVGAYGSERTPQSLQDFPVVHS

Parental  EEEAEEEFQKELSQWRKDPSGSKKKPKYSYKTVEELKAKGRVSKKLTAPQKELSQVKVIDMTGREQKVYY
          .EEAEE.FQKELSQWR..PSGSKKKPKY.YKTVEELKAKGRVSK.LTAP.KELSQVKVIDMTGREQKVY.
Retrocopy KEEAEE-FQKELSQWRQGPSGSKKKPKYFYKTVEELKAKGRVSKQLTAPEKELSQVKVIDMTGREQKVYF

Parental  SYSQISHKHSVPDDGLPLQSPQPPQPGKEAKAPGFALPELEHNLQLLIDLTEQEIIQNDRQLQYERDMVV
          SYSQISHKH.VP.DGL.LQSPQPPQPGKEAKAPGFALPELEHNLQLLIDLTEQEIIQNDRQLQYERDMVV
Retrocopy SYSQISHKHNVPGDGLLLQSPQPPQPGKEAKAPGFALPELEHNLQLLIDLTEQEIIQNDRQLQYERDMVV

Parental  NLSHELEKMSEVLDHEERLISNLSKVLEMVEECERRMQPNCSDPLTLDECARVFETLQDKYYEEYRMSDR
          NLSHELEKMSEVLDHEERLIS.LSKVLEMVEECER.MQPNCSDPLTLD.C...FETL.DKYYE.Y.MS.R
Retrocopy NLSHELEKMSEVLDHEERLISKLSKVLEMVEECERCMQPNCSDPLTLDGCTHIFETLRDKYYEDYWMSHR

Parental  VDLAVAIVYPLMKEYFKEWDPLKDCTYGTEIISKWKSLLENDQLLSHGGQDLSADAFHRLIWEVWMPFVR
          VDL.VAIVYPLMKEYFKEWDPLKDCTYGTEIISKWKSLLENDQLLSHG.QDL.ADAFHRLIWEVWMP.VR
Retrocopy VDLTVAIVYPLMKEYFKEWDPLKDCTYGTEIISKWKSLLENDQLLSHGEQDLLADAFHRLIWEVWMPLVR

Parental  NIVTQWQPRNCDPMVDFLDSWVHIIPVWILDNILDQLIFPKLQKEVENWNPLTDTVPIHSWIHPWLPLMQ
          NIVTQWQPRNCDPMVDFLDSWVHIIPVWILD.ILDQLIFPKLQKEVENWNPLTDT.PIHSWIHPWLPLMQ
Retrocopy NIVTQWQPRNCDPMVDFLDSWVHIIPVWILDTILDQLIFPKLQKEVENWNPLTDTIPIHSWIHPWLPLMQ

Parental  ARLEPLYSPIRSKLSSALQKWHPSDSSAKLILQPWKEVFTPGSWEAFMVKNIVPKLGMCLGELVINPHQQ
          ARLE.LYS.IRSKLS.ALQKWHPSDSSAKLILQPWKEVFTPGSWEAFMVKNIVPKL.MCLGELVINPHQQ
Retrocopy ARLERLYSSIRSKLSRALQKWHPSDSSAKLILQPWKEVFTPGSWEAFMVKNIVPKLEMCLGELVINPHQQ

Parental  HMDAFYWVIDWEGMISVSSLVGLLEKHFFPKWLQVLCSWLSNSPNYEEITKWYLGWKSMFSDQVLAHPSV
          HMDAFYWVI.WEGMISVSSLVGLLEKHFFPKWLQVLCSWLSNSPNYE.ITKWYLGWKS.FSDQVLAH.SV
Retrocopy HMDAFYWVITWEGMISVSSLVGLLEKHFFPKWLQVLCSWLSNSPNYEAITKWYLGWKSVFSDQVLAHLSV

Parental  KDKFNEALDIMNRAVSSNVGAYMQPGARENIAYLTHTERRKDFQYEAMQERREAENMAQRGIGVAASSVP
          .DKFNEALDIMNRAVSSNVGAYMQPGARENIAYLTH.ERRKDFQYEAMQERREAENMAQRGIG.AA.S.P
Retrocopy NDKFNEALDIMNRAVSSNVGAYMQPGARENIAYLTHVERRKDFQYEAMQERREAENMAQRGIGMAAGSMP

Parental  MNFKDLIETKAEEHNIVFMPVIGKRHEGKQLYTFGRIVIYIDRGVVFVQGEKTWVPTSLQSLIDMAK
          MNFKDLIETKAEEHNIVFMP.IGKRHEGKQLYTFG.IV.YIDRGVVF.QG.KTWVPTSLQSLIDMAK
Retrocopy MNFKDLIETKAEEHNIVFMPIIGKRHEGKQLYTFGPIVMYIDRGVVFIQGKKTWVPTSLQSLIDMAK

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	0.18 RPM	28.81 RPM
SRP021940_cerebellum	0.26 RPM	92.96 RPM
SRP021940_embryo	0.61 RPM	143.95 RPM
SRP021940_placental_villous	0.34 RPM	96.41 RPM
SRP021940_synovial_membrane	0.71 RPM	122.55 RPM
SRP021940_testis	11.45 RPM	120.98 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_65 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_65 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_65 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016242	1 retrocopy	retro_ecab_65 ,
Myotis lucifugus	ENSMLUG00000008015	1 retrocopy	retro_mluc_1721,
Monodelphis domestica	ENSMODG00000010710	1 retrocopy	retro_mdom_49,