RetrogeneDB ID: retro_ecab_979

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:79442038..79443017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLUL
• Ensembl ID: ENSECAG00000015865
• Aliases: None
• Description: glutamate-ammonia ligase [Source:HGNC Symbol;Acc:4341]

Sequence

>retro_ecab_979
GACAGGGAGCCCAAGTGTGTAGAAGAGCTGCCTGAGTGGAATTTTGATGGCTCTAGGACTTTTCAGTCTGAAGGCTCCAA
TAGTGACATGTATCTCGTCCCTGCTGCTGTGTTTTGGGACCCTTTCCACAAGGACCCCAACAAGCTGTTGTTCTGTGAAG
TCTTCAAGTACAACTGAAAGTCTACAGAGACCAACTTAAGGCACACCTGTAAACGGATAATGGACATGGAGAGCCACCCG
TCCCCCCCGGTTTGGAACGGAGCAGGAATAAATGCTCATGGGCATAGATGGGCAACCTTCTGGTTGGGCTTCCAATGGCT
TCCCTGGGTCCCAATGTCCATACTACTGTGGTGTGGGAGCAGACAAAGCTTATGGCAGGGATAGTGTGGAGGTTTACTAC
CGGGCCTGCTTGTACGCCAGCGTCAAGATTGCAGGGAGAAATGCCGAGGTCATGCCTGCCCAGTGGGAATTCCAGATAGG
ACCCTGTGAAGGAATCGACATGGGAGATCATCTCTAGGTGGCCCATTTCATCTTGCATTGTGTGTGTCAAGACTTTGGAG
TGATAGTAACCTTTGATCCTAAGCCCATTCCTGGGAAGTAGAAGGGTGCAGGCTGCCACACCAACTTCAGCACCAAGGCC
ACGCGAGAGGAGAATGGTCTGAAGTACACTGGGGAGGCCACTGAGAAACTGAGCAAGAAGCATCAGTACCACATCCGAGC
CTACGATCCCAAGGGGGGCTTGGACAATGCCCGGTGCCTGACTGGATTCCACGAAACCTCCAACATCAATGACATTTCTG
CTGGCGTGGCCAACCATAGTGCTAGCATCCACACTCCCCAGGCCGTCAGCCAGGAAAAGATGGGTTACTTTGAAGACTGT
TGCCCCTCTGCCAACTGTGACCCCTTTTCGGTGACAGAAGCCCTCATCCACATGTGTTTTCTCAACGAAACTGGTGATGA
GCCCTTCCAATACAAAAAC

Alignment

ORF - retro_ecab_979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.57 %
• Parental protein coverage: 85.79 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSEPKCVEELPEWNFDGSSTFQSEGSNSDMYLVPAAMFRDPFRKDPNKLVFCEVFKYNRKPAETNLRHTC
          D.EPKCVEELPEWNFDGS.TFQSEGSNSDMYLVPAA.F.DPF.KDPNKL.FCEVFKYN.K..ETNLRHTC
Retrocopy DREPKCVEELPEWNFDGSRTFQSEGSNSDMYLVPAAVFWDPFHKDPNKLLFCEVFKYN*KSTETNLRHTC

Parental  KRIMDMVSN-QHPWFGMEQEYTLMGTDGHPFGWPSNGFPGPQGPYYCGVGADKAYGRDIVEAHYRACLYA
          KRIMDM.S....P.FG.EQE..LMG.DG.P.GW.SNGFPG.Q.PYYCGVGADKAYGRD.VE..YRACLYA
Retrocopy KRIMDMESH>RPPRFGTEQE*MLMGIDGQPSGWASNGFPGSQCPYYCGVGADKAYGRDSVEVYYRACLYA

Parental  GVKIAGTNAEVMPAQWEFQIGPCEGIDMGDHLWVARFILHRVCEDFGVIVTFDPKPIPGNWNGAGCHTNF
          .VKIAG.NAEVMPAQWEFQIGPCEGIDMGDHL.VA.FILH.VC.DFGVIVTFDPKPIPG...GAGCHTNF
Retrocopy SVKIAGRNAEVMPAQWEFQIGPCEGIDMGDHL*VAHFILHCVCQDFGVIVTFDPKPIPGK*KGAGCHTNF

Parental  STKAMREECGLKYIEEAIEKLSKRHQYHIRAYDPKGGLDNARRLTGFHETSNINDFSAGVANRGASIRIP
          STKA.REE.GLKY..EA.EKLSK.HQYHIRAYDPKGGLDNAR.LTGFHETSNIND.SAGVAN..ASI..P
Retrocopy STKATREENGLKYTGEATEKLSKKHQYHIRAYDPKGGLDNARCLTGFHETSNINDISAGVANHSASIHTP

Parental  RTVGQEKKGYFEDRRPSANCDPFSVTEALIRTCLLNETGDEPFQYKN
          ..V.QEK.GYFED..PSANCDPFSVTEALI..C.LNETGDEPFQYKN
Retrocopy QAVSQEKMGYFEDCCPSANCDPFSVTEALIHMCFLNETGDEPFQYKN

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	0.12 RPM	111.74 RPM
SRP021940_cerebellum	0.93 RPM	1016.42 RPM
SRP021940_embryo	0.38 RPM	161.18 RPM
SRP021940_placental_villous	0.53 RPM	323.50 RPM
SRP021940_synovial_membrane	0.41 RPM	263.29 RPM
SRP021940_testis	2.43 RPM	524.14 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_979 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_979 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013631	4 retrocopies	retro_btau_1050, retro_btau_1474, retro_btau_336, retro_btau_824,
Canis familiaris	ENSCAFG00000013102	2 retrocopies	retro_cfam_1691, retro_cfam_2143,
Callithrix jacchus	ENSCJAG00000004654	1 retrocopy	retro_cjac_2837,
Dasypus novemcinctus	ENSDNOG00000013948	4 retrocopies	retro_dnov_1386, retro_dnov_1870, retro_dnov_2393, retro_dnov_842,
Equus caballus	ENSECAG00000015865	1 retrocopy	retro_ecab_979 ,
Echinops telfairi	ENSETEG00000008329	3 retrocopies	retro_etel_143, retro_etel_189, retro_etel_1968,
Felis catus	ENSFCAG00000010551	1 retrocopy	retro_fcat_1811,
Homo sapiens	ENSG00000135821	4 retrocopies	retro_hsap_2364, retro_hsap_3255, retro_hsap_848, retro_hsap_935,
Gorilla gorilla	ENSGGOG00000024712	3 retrocopies	retro_ggor_1794, retro_ggor_2216, retro_ggor_754,
Loxodonta africana	ENSLAFG00000000700	1 retrocopy	retro_lafr_196,
Macropus eugenii	ENSMEUG00000001774	6 retrocopies	retro_meug_1013, retro_meug_1394, retro_meug_1561, retro_meug_409, retro_meug_433, retro_meug_746,
Macaca mulatta	ENSMMUG00000022884	2 retrocopies	retro_mmul_2047, retro_mmul_954,
Monodelphis domestica	ENSMODG00000006787	4 retrocopies	retro_mdom_1268, retro_mdom_488, retro_mdom_823, retro_mdom_892,
Mus musculus	ENSMUSG00000026473	3 retrocopies	retro_mmus_1730, retro_mmus_1767, retro_mmus_696,
Nomascus leucogenys	ENSNLEG00000018007	3 retrocopies	retro_nleu_1388, retro_nleu_293, retro_nleu_416,
Pongo abelii	ENSPPYG00000000440	1 retrocopy	retro_pabe_2698,
Pan troglodytes	ENSPTRG00000001751	4 retrocopies	retro_ptro_2201, retro_ptro_2823, retro_ptro_589, retro_ptro_647,
Sarcophilus harrisii	ENSSHAG00000000116	1 retrocopy	retro_shar_553,
Sus scrofa	ENSSSCG00000015545	1 retrocopy	retro_sscr_726,
Ictidomys tridecemlineatus	ENSSTOG00000014529	2 retrocopies	retro_itri_1083, retro_itri_743,
Tupaia belangeri	ENSTBEG00000003522	3 retrocopies	retro_tbel_2230, retro_tbel_3079, retro_tbel_3992,
Tarsius syrichta	ENSTSYG00000002066	1 retrocopy	retro_tsyr_385,
Tursiops truncatus	ENSTTRG00000010781	1 retrocopy	retro_ttru_543,
Drosophila melanogaster	FBgn0001145	1 retrocopy	retro_dmel_44,