RetrogeneDB ID: retro_ecab_277

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:11866988..11867644(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD1
• Ensembl ID: ENSECAG00000006587
• Aliases: None
• Description: RWD domain containing 1 [Source:HGNC Symbol;Acc:20993]

Sequence

>retro_ecab_277
TCATTATCTGGAATTACCAGGAAACCCCCCAGCTTCACCATCACTCTGACATCTGAGGCTGGAGAAAACAGCAAACCTGT
CCAGACCACATTCAAGTTCACGTACAGTGAAAAACACCCGGATGAAGCCCCCTTAATGCAATATTCTCCCAGGAAAATAT
CTAGAAGACAAGGATGTCTCCGGCACTTTAAAATTATTAGCACTACAGGCAGAAGAAACCCTTGGCATGGTGATGATTTT
TACTTTAGTGTTGGCTGCACACGAAAAATTATATGAAATAGTAGATCAAATCAAAACCAGAAGAAAGGCAGGAAGACAAG
ATACAAAACGGGAAGAAAGTAGGAGCCAAAAAGCAATTATTTCATGGTGCTCCTGTTACGATTGAGAATTTCTTAAGTTG
CAAGGCCAGGTTTAATGCAAGACTCTTGGAAATTAAAAAGAAACGTGTGGAAGCAGAACAACAAGCGGGAGAAAGCTGAT
TCGGTGGGAAACAGCGATTCGAATGCTCGTCTCGATTCGTCTTTGACTCTGATGTGTCTGACAGCTGGTTGCACGGGTGC
TGCCAGCACGTGGAGGTGGACGAGGCTCTGCGCCGGGAACCGGCAGACTTGGAGCTGGAGCATGCCCATGGTCCAGGCTG
CAATCCTGCTGACCCG

Alignment

ORF - retro_ecab_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.73 %
• Parental protein coverage: 88.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SFTVLSENPPSFTITVTSEAGENDETVQTTLKFTYSEKYPDEAPLYE-IFSQENLEDNDVSDILKLLALQ
          S.......PPSFTIT.TSEAGEN...VQTT.KFTYSEK.PDEAPL...I.....LED.DVS..LKLLALQ
Retrocopy SLSGITRKPPSFTITLTSEAGENSKPVQTTFKFTYSEKHPDEAPLMQ>ILPGKYLEDKDVSGTLKLLALQ

Parental  AEENLGMVMIFTLVTAVQEKLNEIVDQIKTRREEEKKQKEKEAEE-AEKQLFHGTPVTIENFLSWKAKFD
          AEE.LGMVMIFTLV.A..EKL.EIVDQIKTRR.........E....A.KQLFHG.PVTIENFLS.KA.F.
Retrocopy AEETLGMVMIFTLVLAAHEKLYEIVDQIKTRRKAGRQDTKREESR>AKKQLFHGAPVTIENFLSCKARFN

Parental  AELLEIKKKRMKEEEQAGKNKLSGKQLFE-TDHNLDTSDI--QFLEDAGNNVEVDESLFQEMDDLELEDD
          A.LLEIKKKR...E.QAG.....GKQ.FE........SD.....L......VEVDE.L..E..DLELE..
Retrocopy ARLLEIKKKRVEAEQQAGES*FGGKQRFECSSRFVFDSDVSDSWLHGCCQHVEVDEALRREPADLELE-H

Parental  EDDPDYNPADP
          ...P..NPADP
Retrocopy AHGPGCNPADP

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	10.21 RPM
SRP021940_cerebellum	0.05 RPM	11.84 RPM
SRP021940_embryo	0.33 RPM	21.99 RPM
SRP021940_placental_villous	0.00 RPM	16.26 RPM
SRP021940_synovial_membrane	0.03 RPM	15.07 RPM
SRP021940_testis	0.00 RPM	36.90 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_277 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_277 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
Ailuropoda melanoleuca	ENSAMEG00000005692	1 retrocopy	retro_amel_991,
Bos taurus	ENSBTAG00000009689	1 retrocopy	retro_btau_1004,
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622,
Equus caballus	ENSECAG00000006587	2 retrocopies	retro_ecab_216, retro_ecab_277 ,
Echinops telfairi	ENSETEG00000019085	3 retrocopies	retro_etel_140, retro_etel_1992, retro_etel_423,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691,
Procavia capensis	ENSPCAG00000005016	1 retrocopy	retro_pcap_114,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986, retro_tbel_4366,