RetrogeneDB ID: retro_ecab_912

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:70013026..70014035(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSECAG00000007190
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H3 (2H9) [Source:HGNC Symbol;Acc:5043]

Sequence

>retro_ecab_912
ATGGATTGGGTTATGAAACATAATGGTCCAAATGACGTTAGTGATGGGACAGTACAATTTGTGGACTGCCATTTGATTGC
AGCAAAGAGGAAATAGTTCAGTTCTTTCAAGGGTTGGAAATCGTACCAAATGGGATAACGTTGATGATGCACTACAAGGG
GAGGAGCACAGGGGAGGCCTTCGTGCAGTTTGCTTCAAAGGAGATGGCAGAAAATGCTCCGGGGAAATCAAGGAAAGAAT
AGGGCACAGGTATGTTCAGATCTTCAAAAGCATCAGGAGTGAAATCAAAGGATTTTATGATCCACCAAGAAGATTGCTGG
GCCAGCGACCGGGACCATATGATAGACCAATAGGAGGAAGAGGGGGTTATTATGGAGCTGGGAGTGGAAGTATGTATGAC
AGAATGCGATCAAGAGGTGATGGGTATGATGGTGGTTATGGAGGTTTTGATGACTGTGGTGGCTATAATAATTATGGCTG
TGGAGATGATGGCTTCGATGACAGAATGAGAGATGGAAGAGGTATGGGAGGACATGGCTATGGTGGAGCTGGTGATGCCA
GTTCAGGTTTCCATGGTGGTCATTTTGTACATATGAGAGGATTGCCTTTTCGTGCAACTGAAAATGATGTTGCTAGTTTT
TTCTCACCACTAAATCCAATATGAGTGCATGTTGGTATTGGAGCTGATGGCAGAGCAACAGGAGAAGCAGATGTAGAGTT
TGTGACACATGAAGATGCAGTAGCTGCCATATGTAAAGATAAGAATAACATGCAACATCGATACATTGAACTCTTCTGGA
ATTCGACTCCTGGAGGTGGCTCTGGAATGGGAGGTTCTGGAATGGGAGGCTACGGCAGAGATGGAATAGATAATCAAGGA
GGTTATGGCTCTGTTGGAAGAATGGGAACGGGGAACTGTTACAGTGGAGGCTATGGCACTCCTGATGGCTTGAGTGGTTA
TGGCCCCGGTGGTGGAGGCAATGGAGGTTGTATGGGTAAGGACGGCGTG

Alignment

ORF - retro_ecab_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.61 %
• Parental protein coverage: 97.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDWVMKHNGPNDASDGTVR-LRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRSTGEAFVQFASKEI
          MDWVMKHNGPND.SDGTV....GLPF.CSKEEIVQFFQGLEIVPNGITL.M.Y.GRSTGEAFVQFASKE.
Retrocopy MDWVMKHNGPNDVSDGTVQ<ICGLPFDCSKEEIVQFFQGLEIVPNGITLMMHYKGRSTGEAFVQFASKEM

Parental  AENALGKH-KERIGHRYIEIFRSSRSEIKGFYDPPRRLLGQRPGPYDRPIGGRGGYYGAGRGSMYDRMRR
          AENA.GK..KERIGHRY..IF.S.RSEIKGFYDPPRRLLGQRPGPYDRPIGGRGGYYGAG.GSMYDRMR.
Retrocopy AENAPGKS<KERIGHRYVQIFKSIRSEIKGFYDPPRRLLGQRPGPYDRPIGGRGGYYGAGSGSMYDRMRS

Parental  GGDGYDGGYGGFDDYGGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATE
          .GDGYDGGYGGFDD.GGYNNYG.G.DGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATE
Retrocopy RGDGYDGGYGGFDDCGGYNNYGCGDDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATE

Parental  NDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNSTPGGGSGMG
          ND.A.FFSPLNPI.VH..IGADGRATGEADVEFVTHEDAVAA..KDKNNMQHRYIELF.NSTPGGGSGMG
Retrocopy NDVASFFSPLNPI*VHVGIGADGRATGEADVEFVTHEDAVAAICKDKNNMQHRYIELFWNSTPGGGSGMG

Parental  GSGMGGYGRDGMDNQGGYGSVGRMGMGNNYSGGYGTPDGLGGYGRGGGGSGGYYGQGGM
          GSGMGGYGRDG.DNQGGYGSVGRMG.GN.YSGGYGTPDGL.GYG.GGGG.GG..G..G.
Retrocopy GSGMGGYGRDGIDNQGGYGSVGRMGTGNCYSGGYGTPDGLSGYGPGGGGNGGCMGKDGV

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	24.79 RPM
SRP021940_cerebellum	0.00 RPM	30.95 RPM
SRP021940_embryo	0.26 RPM	131.06 RPM
SRP021940_placental_villous	0.10 RPM	60.48 RPM
SRP021940_synovial_membrane	0.03 RPM	36.46 RPM
SRP021940_testis	0.06 RPM	61.64 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_912 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_912 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912 ,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,