RetrogeneDB ID: retro_ecab_123

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:37496714..37497205(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSECAG00000019556
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 9 [Source:HGNC Symbol;Acc:8056]

Sequence

>retro_ecab_123
CAGTACACTGCAGGCTCTTTCTTGGTCTGATCCATGAGGGCACGCACCCAAGTACTTGAAAGGAACTTCTCTCCTAAATT
TAATGAAAGGGTGGGCTCGTTGAGAGAGGGAGCCAGAATGGTTTGTATGAGGTTGAAAATGGTAAACCTAGAAATCCTGC
AGGTCAGATACAGCTGGTTGCCTGAGGGCTTTGGGGATGTTGGGTCCTCAATCATCCTGCAGCTCCCATCTTAACCAGGT
GGAACAAGGATAGCAAGGGAAATAAAGTTACCCACCCTGTTTCTGGGAGAAGCATCCTGCAATTTGTAGCCATCAGGAGG
AAGGACTGTGGAAACTGGGCCATCCCACGGGGGATGGTGGATCCATGAGAGGTTAGTACCACAATGAGGAGAGAATTTGG
TAAGGAAGCCATAATCTCCTTACAGAAATCCAGAGCAGAAAGTCAGAAGTTGGAGAAACGATTGAAGAAACTATTCAGCC
ATGACATTTTG

Alignment

ORF - retro_ecab_123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.05 %
• Parental protein coverage: 77.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYTAVSVLAGPRWADPQISESTFSPKFNE-KDGHVERKSQNGLYEIENGRPRNPAGRTGLVGRGLLGRWG
          .YTA.S.L.....A..Q..E..FSPKFNE.K.G.VER.SQNGLYE.ENG.PRNPAG...LV..GL.G.W.
Retrocopy QYTAGSFLV*SMRARTQVLERNFSPKFNE<KGGLVERGSQNGLYEVENGKPRNPAGQIQLVA*GLWGCWV

Parental  PNHAADPIITRWKRDRSGNKITHPISGKNILQFVAIKRKDCGEWAIPGGMVDPGEKISAALKREFGEEAL
          .NH.A.PI.TRW..D..GNK.THP.SG..ILQFVAI.RKDCG.WAIP.GMVDP.E..S....REFG.EA.
Retrocopy LNHPAAPILTRWNKDSKGNKVTHPVSGRSILQFVAIRRKDCGNWAIPRGMVDP*E-VSTTMRREFGKEAI

Parental  NSLQKSSAEKRELEEQLQKLFSQEHL
          .SLQKS.AE...LE..L.KLFS...L
Retrocopy ISLQKSRAESQKLEKRLKKLFSHDIL

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	16.00 RPM
SRP021940_cerebellum	0.00 RPM	19.53 RPM
SRP021940_embryo	0.00 RPM	17.08 RPM
SRP021940_placental_villous	0.00 RPM	20.64 RPM
SRP021940_synovial_membrane	0.00 RPM	16.75 RPM
SRP021940_testis	0.00 RPM	81.53 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_123 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_123 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_123 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_709
Pan troglodytes	retro_ptro_506
Gorilla gorilla	retro_ggor_602
Pongo abelii	retro_pabe_613
Callithrix jacchus	retro_cjac_1047
Oryctolagus cuniculus	retro_ocun_990
Bos taurus	retro_btau_1112
Sus scrofa	retro_sscr_447
Canis familiaris	retro_cfam_1271

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003244	1 retrocopy	retro_amel_612,
Bos taurus	ENSBTAG00000011354	1 retrocopy	retro_btau_1112,
Canis familiaris	ENSCAFG00000009529	1 retrocopy	retro_cfam_1271,
Callithrix jacchus	ENSCJAG00000006159	1 retrocopy	retro_cjac_1047,
Equus caballus	ENSECAG00000019556	1 retrocopy	retro_ecab_123 ,
Echinops telfairi	ENSETEG00000019164	1 retrocopy	retro_etel_348,
Felis catus	ENSFCAG00000003315	1 retrocopy	retro_fcat_1509,
Homo sapiens	ENSG00000170502	1 retrocopy	retro_hsap_709,
Gorilla gorilla	ENSGGOG00000014777	1 retrocopy	retro_ggor_602,
Loxodonta africana	ENSLAFG00000011391	1 retrocopy	retro_lafr_224,
Macropus eugenii	ENSMEUG00000012123	4 retrocopies	retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica	ENSMODG00000020738	2 retrocopies	retro_mdom_157, retro_mdom_706,
Mustela putorius furo	ENSMPUG00000002258	1 retrocopy	retro_mputfur_585,
Nomascus leucogenys	ENSNLEG00000009520	1 retrocopy	retro_nleu_464,
Oryctolagus cuniculus	ENSOCUG00000002670	2 retrocopies	retro_ocun_1045, retro_ocun_990,
Ochotona princeps	ENSOPRG00000004055	1 retrocopy	retro_opri_1152,
Pongo abelii	ENSPPYG00000014914	1 retrocopy	retro_pabe_613,
Pan troglodytes	ENSPTRG00000016259	1 retrocopy	retro_ptro_506,
Pteropus vampyrus	ENSPVAG00000004829	1 retrocopy	retro_pvam_475,
Sus scrofa	ENSSSCG00000009223	1 retrocopy	retro_sscr_447,
Tursiops truncatus	ENSTTRG00000004207	1 retrocopy	retro_ttru_1549,
Vicugna pacos	ENSVPAG00000004012	1 retrocopy	retro_vpac_125,