RetrogeneDB ID: retro_ecab_886

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:66204470..66205286(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000007371
• Aliases: None
• Description: Glutamate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F6V4L4]

Sequence

>retro_ecab_886
CAAGTTTCTTATATGAGCATTTTAGGAATTAAACCGGAGTTTGTAGATAATACTTTGTTATTCAGGGATTTGGCAATGTG
GGCCTGTACCCTATGAGATCATTACATCATATTGGTGCTAAATGTCTTGGTGTTGGTGAATCTAGTGGGAGCATGTGGAA
TTTAGATGGCATTGACTCAAAGAAGCTAGAAGACTTCAAATTGCAATGTGGATCAATCCTGGGTTTCCCCAAGGCAAAGC
CCTAGGAAGGAAATGTCTTCTAAGCAGACTGTGACATACTAATCCCTGCTGTCAATGAGAAGCAGTTGACCAAATCCGGG
GCATCCAGAGTCAAAAGCCAGGATTGTTGCTGAAGCTGCCAAAGGACCGACAACTCTAGAAGCTGATGAGATTTTTTTGG
AGAGGAACGTTATGGTTATTCCTGATCTCCTCTTAAATGCTGGTACAATGACAGTATCTTAGTTGGAGTGGCTGAAGAAC
ATAAATCATGTCAGCTATGGCCATTTGAGCTTCAAGTATGAAAGAGATTCTAACTACCACTTCCTCATGTCTATTCACAG
GAGTTTAGAAAGAAAATTTGGAAACCACCATGGAACTATTTCCGTCGTAACCACAGCAGGGTTCCAAAACAGAATATCAG
GTACATCTGAGAAAGACATCGTGCATTCTGGCTTACCTTACACTATGGAGTTTTCTGCCTGGCAAATCATGCCCAGCACC
ACAAAGTATAACCTAGGATTGGATCTGAGAACAGCTGCCTATGTCAACAGCATTTAGAAAGTCTTCAGGGTGTACAAGGA
AGCTGGTTTGACCTTC

Alignment

ORF - retro_ecab_886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.09 %
• Parental protein coverage: 54.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EASYMSILGMTPGFGDKT-FVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELEDFKLQ
          ..SYMSILG..P.F.D.T.FV.QGFGNVGL..MR.LH..GAKC..VGES.GS.WN.DGID.K.LEDFKLQ
Retrocopy QVSYMSILGIKPEFVDNT<FVIQGFGNVGLYPMRSLHHIGAKCLGVGESSGSMWNLDGIDSKKLEDFKLQ

Parental  HGSILGFPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVK-AKIIAEGANGPTTPEADKIFLERNIM
          .GSILGFPKAKP.EG....ADCDILIPA..EKQLTKS.A.RVK.A.I.AE.A.GPTT.EAD.IFLERN.M
Retrocopy CGSILGFPKAKP*EGNVF*ADCDILIPAVNEKQLTKSGASRVK>ARIVAEAAKGPTTLEADEIFLERNVM

Parental  VIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEF
          VIPDL.LNAG..TVS..EWLKN.NHVSYG.L.FKYERDSNYH.LMS...SLERKFG.H.GTI..V.TA.F
Retrocopy VIPDLLLNAGTMTVS*LEWLKNINHVSYGHLSFKYERDSNYHFLMSIHRSLERKFGNHHGTISVVTTAGF

Parental  QDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTF
          Q.RISG.SEKDIVHSGL.YTME.SA.QIM....KYNLGLDLRTAAYVN.I.KVF.VY.EAG.TF
Retrocopy QNRISGTSEKDIVHSGLPYTMEFSAWQIMPSTTKYNLGLDLRTAAYVNSI*KVFRVYKEAGLTF

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	78.57 RPM
SRP021940_cerebellum	0.00 RPM	182.23 RPM
SRP021940_embryo	0.00 RPM	119.42 RPM
SRP021940_placental_villous	0.00 RPM	83.52 RPM
SRP021940_synovial_membrane	0.00 RPM	120.24 RPM
SRP021940_testis	2.43 RPM	19.50 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_886 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_886 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886 , retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,