RetrogeneDB ID: retro_ecab_565

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:26072618..26073039(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP3
• Ensembl ID: ENSECAG00000018299
• Aliases: None
• Description: FK506 binding protein 3, 25kDa [Source:HGNC Symbol;Acc:3719]

Sequence

>retro_ecab_565
CAGAACATGTTATTAAGAAACTTTAAAAATGTGGCTAAAACAGCTAACAAGGACCATTTGGTTACAGCCTATAACCATCT
CTATGAAAGCAAGCGTTTCAAGGGTACTGAAAGTCTAAGTAACGTGTGCAAGGAGGTGAAAAATTGGAAGCTTACTGAAG
ATAAACCGGAAGAAATCAAGTTTGAAGAGTCTCTGAATGGGGGTCCACCGAAATATACAAAATCTGTCCTTAAAAAAGGA
GATGAAACCAACTTTCCCAAAAAGGGAGATGTTGTTCACTGCTGATATACAAGAGTAAGACACGATGGCACTGTTTCTGA
TACTAATATTCAAACAAGTTCAAAGAAGAAGAAAAGCACCAAGCCTTGTAAATTTTAAGGTTGGAATAGGCAAAATTATC
AGAGGATTGGATGAAGTCTTA

Alignment

ORF - retro_ecab_565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.89 %
• Parental protein coverage: 74.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EHKLLGNIKNVAKTANKDHLVTAYNHLFESKRFKGTESVSKVSEQVKNVKLNEDKPKETKSEETLDEGPP
          ...LL.N.KNVAKTANKDHLVTAYNHL.ESKRFKGTES.S.V...VKN.KL.EDKP.E.K.EE.L..GPP
Retrocopy QNMLLRNFKNVAKTANKDHLVTAYNHLYESKRFKGTESLSNVCKEVKNWKLTEDKPEEIKFEESLNGGPP

Parental  KYTKSVLKKGDKTNFPKKGDVVHCWYTGTLQDGTVFDTNIQTSSKKKKNAKP-LSFKVGIGKVIRGWDEA
          KYTKSVLKKGD.TNFPKKGDVVHC.YT....DGTV.DTNIQTSSKKKK..KP...FKVGIGK.IRG.DE.
Retrocopy KYTKSVLKKGDETNFPKKGDVVHC*YTRVRHDGTVSDTNIQTSSKKKKSTKP>VNFKVGIGKIIRGLDEV

Parental  L
          L
Retrocopy L

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	0.06 RPM	7.50 RPM
SRP021940_cerebellum	0.00 RPM	15.68 RPM
SRP021940_embryo	0.00 RPM	41.86 RPM
SRP021940_placental_villous	0.00 RPM	17.85 RPM
SRP021940_synovial_membrane	0.00 RPM	10.98 RPM
SRP021940_testis	0.00 RPM	29.35 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_565 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_565 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_565 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616, retro_cfam_798,
Choloepus hoffmanni	ENSCHOG00000000189	1 retrocopy	retro_chof_2315,
Equus caballus	ENSECAG00000015664	1 retrocopy	retro_ecab_752,
Equus caballus	ENSECAG00000018299	2 retrocopies	retro_ecab_352, retro_ecab_565 ,
Echinops telfairi	ENSETEG00000003358	8 retrocopies	retro_etel_1114, retro_etel_1484, retro_etel_1491, retro_etel_1499, retro_etel_1774, retro_etel_2130, retro_etel_2200, retro_etel_997,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Procavia capensis	ENSPCAG00000011316	2 retrocopies	retro_pcap_454, retro_pcap_78,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,
Tarsius syrichta	ENSTSYG00000002125	2 retrocopies	retro_tsyr_515, retro_tsyr_820,