RetrogeneDB ID: retro_ecab_291

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:1979931..1981872(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA8
• Ensembl ID: ENSECAG00000013510
• Aliases: None
• Description: Heat shock cognate 71 kDa protein [Source:UniProtKB/Swiss-Prot;Acc:A2Q0Z1]

Sequence

>retro_ecab_291
ACCATGTCTGAGGGACCTGCAGTTGGCATTGATCTTGGCACCACCTACTCGTGTGTGGGTGTTTTCCAGCATGGAAAAGT
GGAAATAATAGCCAATGATCAAGGAAACCGAACCACCCCAAGCTATGTCGCTTTTACTGACACGGAACGATTGATCGGTG
ATGCTGCAAAGAACCAAGTTGCAACGAACCCGACCAACACGGTTTTTGATGCCAAACGTCTGATTGGACGTAGATTTGAT
GATGCTGTTGTCCAGTCTGATATGAAGCATTGGCCCTTCATGGTGGTGAATGATGCAGGCAGGCCCAAGGTCCAAGTAGA
ATACAAGGGAGAGACAAAAAGTTTCTATCCAGAGGAGGTGTCTTCTATGGTTTTGACAAAGATGAAGGAAATCACAGAAG
CCTACCTTGGGAAGACTGTTACCAATGCTGTTGTCACAGTACCTGCTTACTTTAATGACTCTCAGCGTCAGGCTACCAAA
GATGCTGGAACTATTGCTGGTCTCAATGTACTTAGAATCATCAATGAGCCAACTGCTGCTGCTATTGCTTACGGTTTAGA
CAAAAAGGTTGGAGCTGAGAGAAACGTACTGACCTTTGACTTAGGAGGTGGCACTTTCGATGTGTCAATCCTCTCTATTG
AAGATGGAATCTTTGAGGTCAAATCTACAGCTGGAGACACCCACTTAAGTGGAGAAGACTTTGACAACTGAATGGTCAAC
CATTTTATCGCAGAATTCAAGCGCAAGCATAAGAAGGACATCAGTGAGAACAAGAGGGCCGTCCGACGCCTGCGCACTTC
TTGTGAACGTGCTAAGCGTACTCTCTCTTCTAGCACCCAGGCCAGTATTGAGATTGATTCACTCTATGAAGGAATCGACT
TCTATACCTCTATTACCCGTGCCCGATTTGAAGAATTGAATGCTGACCTGTTCCGTGGCACCCTGGACCCTGTAGAGAAA
GCCCTTCGGGATGCCAAGCTGGACAAGACCCAGATTCATGATATTGTCCTAGTGGGTGGTTCTACCTGCATCCCCAAGAT
TCAGAAACTTCTACAGGACTTCTTCAATGGAAAAGAACTGAATAAGAGCATCAACCCTGATGAGGCTGTTGCTTATGGTG
CAGCTGTCCAGGCAGCCATCCTATCTGGAGACAAATCTGAAAATGTTCAAGATTTGCTGCTGTTGGATGTCACTCCTCTT
TCCCTTGGCATGGAAACTGCTGGTGGAGTCATGACTGTGCTCATAAAGTGCAACACTACGATTCCTACCAAGCAGACACA
AACCTTCACTACCTACTCTGACAACCAGCCTGGTGTGCTCATTCAGGTTTATGAAGGTGAGCATGCCATGACCAAGGATA
ACAATCTGCTTGGCAAGTTTGAACTCACAGGCATACCTCCAGCCCCTCGTGGTGTTCCTCAGATTGAAGTCACTTTTGAT
ATTGATGCCAATGGCATTCTCAATGTCTCTGCTGTGGACAAGAGTACAGGGAAAGAAAACAAGATCACCATCACTAACGA
CAAGGGTCGTTTGAGCAAGGAAGACATAGAGTGCATGGTCCAGGAAGCTGAGAAGTACAAGGCTAAAGATGAAAAGCAGC
AGGACAAGGTGTCTTCTAAGAATTCACTTGAGTCCTATGCATTCAACATGAAAGCAACTGTTGAAGATGAAAAACTTCAA
GGCAAGATCAATGACGAGGACAAACAGAAGATTCTTGACAAGCGCAATGAAATCATCAACTGGCTTGACAAGAACCAGAC
TGCAGAGAAGGAAGAATTTGAACATCAGCAGAAAGAGCTGGAGAAAGTTTGCAACTCCATCATTACCAAGCTGTACCAGA
GTGCAGGAAGCATGCCAGGAGGAATGCCTGGGGGTTTCCCTGGTGGTGGAGCTCCTCCATCTGGTGGTGCCTCCTCTGGA
CCCACCATTGAAGAGGTGGAT

Alignment

ORF - retro_ecab_291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFD
          TMS.GPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVA.NPTNTVFD
Retrocopy TMSEGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVATNPTNTVFD

Parental  AKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTV
          AKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEI.EAYLGKTV
Retrocopy AKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEITEAYLGKTV

Parental  TNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSI
          TNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVL.FDLGGGTFDVSI
Retrocopy TNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLTFDLGGGTFDVSI

Parental  LTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQ
          L.IEDGIFEVKSTAGDTHL.GEDFDN.MVNHFIAEFKRKHKKDISENKRAVRRLRT.CERAKRTLSSSTQ
Retrocopy LSIEDGIFEVKSTAGDTHLSGEDFDN*MVNHFIAEFKRKHKKDISENKRAVRRLRTSCERAKRTLSSSTQ

Parental  ASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKL
          ASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDK.QIHDIVLVGGST.IPKIQKL
Retrocopy ASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKTQIHDIVLVGGSTCIPKIQKL

Parental  LQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTT
          LQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLG.ETAGGVMTVLIK.NTT
Retrocopy LQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGMETAGGVMTVLIKCNTT

Parental  IPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
          IPTKQTQTFTTYSDNQPGVLIQVYEGE.AMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
Retrocopy IPTKQTQTFTTYSDNQPGVLIQVYEGEHAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS

Parental  AVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQ
          AVDKSTGKENKITITNDKGRLSKEDIE.MVQEAEKYKA.DEKQ.DKVSSKNSLESYAFNMKATVEDEKLQ
Retrocopy AVDKSTGKENKITITNDKGRLSKEDIECMVQEAEKYKAKDEKQQDKVSSKNSLESYAFNMKATVEDEKLQ

Parental  GKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGGG
          GKINDEDKQKILDK.NEIINWLDKNQTAEKEEFEHQQKELEKVCN.IITKLYQSAG.MPGGMPGGFPGGG
Retrocopy GKINDEDKQKILDKRNEIINWLDKNQTAEKEEFEHQQKELEKVCNSIITKLYQSAGSMPGGMPGGFPGGG

Parental  APPSGGASSGPTIEEVD
          APPSGGASSGPTIEEVD
Retrocopy APPSGGASSGPTIEEVD

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	1.71 RPM	93.27 RPM
SRP021940_cerebellum	4.47 RPM	421.85 RPM
SRP021940_embryo	4.71 RPM	381.14 RPM
SRP021940_placental_villous	2.50 RPM	399.85 RPM
SRP021940_synovial_membrane	7.03 RPM	245.97 RPM
SRP021940_testis	1.02 RPM	210.82 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_291 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_291 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_291 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Equus caballus	ENSECAG00000013510	2 retrocopies	retro_ecab_291 , retro_ecab_628,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Nomascus leucogenys	ENSNLEG00000007419	8 retrocopies	retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175, retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Ictidomys tridecemlineatus	ENSSTOG00000003756	1 retrocopy	retro_itri_51,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,