RetrogeneDB ID: retro_ecab_1121

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:74959267..74960528(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BZW2
• Ensembl ID: ENSECAG00000022038
• Aliases: None
• Description: basic leucine zipper and W2 domains 2 [Source:HGNC Symbol;Acc:18808]

Sequence

>retro_ecab_1121
AGAAATTTTATGACTAAGCATCAGGAGCCAGTGCTAACAGGCCAGCGGTTCAAAACTCAGAAAAGGGATGAAAAAGAGAA
ATTCAAACCCACTGTCTTTAGGGATACACTTGTCCAGAGGCTTAATGAAGATAGGGATGACCTTGAAGCTGTAGCCAAGT
TTCTGGACTCTACAGGCTCAAGATTAGATTATTGTCGCTGTGCAGACACACTCTTCGATATCCTGGTGGCTGGCAGTATG
CTTGCCCCTGGAGGAACACGCATAGATGATGGTGACAAGACGAAGATGACCAACCACTGTGTGTTTTCAGCAAATGAAGA
TCATGAAATCATCTGAAACTATGCTCAGGTCTTCAATAAACTCATCAGGAGATATAAGTATTTGGAAAAGGCATTTGAGG
ATGAAATGAAAAAGCTTCTCTTCTTCCTTAAAGCCTTTTCCAAAACAGAGCAGACAAAGTTGGCAATGCTGTCAGGGATC
CTGCTAGATAATGGCACCCTTCCTGCCACCATCCTTACCAGTCTCTTCACCGACAGCTTAGTCAAGGAAGGCATTGCAGC
CTCATTTGCTGTCAAGCTTTTTAAAGCATGGATGACAGAGAAAGATGCCAACTCTCTGCTCTCTTCTTTGAGAAAAGCCA
ACTTAGACAAGAGGCTACTTGAGCTCTTTCCAGTTAACAGACAGAGTGTGGATCATTTTGCTAAATACTTGCTGATGCAG
GTCTGAAGGAGCTTTCTTACTTCCTGTGAGTCCAGCGGTCCCTAGGCACCAGGAAGGAACTGCAGAAGGAGCTCCAGGAG
TGTCTTTCTCAGGAATGCCCGATTGAGGAGGTGGTGCTCTATGTGAAAGAAGAAATGAAGAGGAATGATCTTCCAAAAAC
AGCAGTGATTGGACTCCTATGGACCTGTATAATGAATGCTGTTGAGTGGAACAAGAAGGAAGACCTCATTGCAGAGCAGG
CCCTTAAACACCTGAGGCAATACGCTCCTCTCCTGGCTGTGTTCAGCTCCCAAGGCCAGTCAGAGCTGATCCTCCTCCAG
AAGGTTCAGGAATACTGTTATGACAACATCCATTTCATGAAAGCCTTTCAGATCTGGTTCTCTTTTATAAAGCTGGTGTG
CTGAGTGAAGAAGCGATATTGAAATGATACAAAGAAGCACATGTTGCCAAAGGCAAGAGTGTTTTTCTTGACCAGATGAA
GAAATTTGTCAAGTGGTTACAAAACGCAGAAGAAGAATCTGAATCGGAAGGCGAGGAAAGT

Alignment

ORF - retro_ecab_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RNFMNKHQKPVLTGQRFKTRKRDEKEKFEPTVFRDTLVQGLNEAGDDLEAVAKFLDSTGSRLDYRRYADT
          RNFM.KHQ.PVLTGQRFKT.KRDEKEKF.PTVFRDTLVQ.LNE..DDLEAVAKFLDSTGSRLDY.R.ADT
Retrocopy RNFMTKHQEPVLTGQRFKTQKRDEKEKFKPTVFRDTLVQRLNEDRDDLEAVAKFLDSTGSRLDYCRCADT

Parental  LFDILVAGSMLAPGGTRIDDGDKTKMTNHCVFSANEDHETIRNYAQVFNKLIRRYKYLEKAFEDEMKKLL
          LFDILVAGSMLAPGGTRIDDGDKTKMTNHCVFSANEDHE.I.NYAQVFNKLIRRYKYLEKAFEDEMKKLL
Retrocopy LFDILVAGSMLAPGGTRIDDGDKTKMTNHCVFSANEDHEII*NYAQVFNKLIRRYKYLEKAFEDEMKKLL

Parental  LFLKAFSETEQTKLAMLSGILLGNGTLPATILTSLFTDSLVKEGIAASFAVKLFKAWMAEKDANSVTSSL
          .FLKAFS.TEQTKLAMLSGILL.NGTLPATILTSLFTDSLVKEGIAASFAVKLFKAWM.EKDANS..SSL
Retrocopy FFLKAFSKTEQTKLAMLSGILLDNGTLPATILTSLFTDSLVKEGIAASFAVKLFKAWMTEKDANSLLSSL

Parental  RKANLDKRLLELFPVNRQSVDHFAKY-FTDAGLKELSDFLRVQQSLGTRKELQKELQERLSQECPIKEVV
          RKANLDKRLLELFPVNRQSVDHFAKY...DAGLKELS.FL.VQ.SLGTRKELQKELQE.LSQECPI.EVV
Retrocopy RKANLDKRLLELFPVNRQSVDHFAKY<LADAGLKELSYFL*VQRSLGTRKELQKELQECLSQECPIEEVV

Parental  LYVKEEMKRNDLPETAVIGLLWTCIMNAVEWNKKEELVAEQALKHLKQYAPLLAVFSSQGQSELILLQKV
          LYVKEEMKRNDLP.TAVIGLLWTCIMNAVEWNKKE.L.AEQALKHL.QYAPLLAVFSSQGQSELILLQKV
Retrocopy LYVKEEMKRNDLPKTAVIGLLWTCIMNAVEWNKKEDLIAEQALKHLRQYAPLLAVFSSQGQSELILLQKV

Parental  QEYCYDNIHFMKAFQ-KIVVLFYKADVLSEEAILKWYKEAHVAKGKSVFLDQMKKFVEWLQNAEEESESE
          QEYCYDNIHFMKAFQ...V....KA.VLSEEAILK.YKEAHVAKGKSVFLDQMKKFV.WLQNAEEESESE
Retrocopy QEYCYDNIHFMKAFQ<DLVLFY-KAGVLSEEAILK*YKEAHVAKGKSVFLDQMKKFVKWLQNAEEESESE

Parental  GEES
          GEES
Retrocopy GEES

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	26.86 RPM
SRP021940_cerebellum	0.05 RPM	23.01 RPM
SRP021940_embryo	0.10 RPM	74.29 RPM
SRP021940_placental_villous	0.10 RPM	42.10 RPM
SRP021940_synovial_membrane	0.08 RPM	32.97 RPM
SRP021940_testis	0.00 RPM	3.20 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1121 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1121 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001663	4 retrocopies	retro_dnov_2177, retro_dnov_2422, retro_dnov_2649, retro_dnov_575,
Equus caballus	ENSECAG00000022038	1 retrocopy	retro_ecab_1121 ,
Macaca mulatta	ENSMMUG00000017045	1 retrocopy	retro_mmul_1457,
Ochotona princeps	ENSOPRG00000005256	2 retrocopies	retro_opri_665, retro_opri_9,
Pongo abelii	ENSPPYG00000017763	1 retrocopy	retro_pabe_2385,
Pteropus vampyrus	ENSPVAG00000014571	1 retrocopy	retro_pvam_481,
Ictidomys tridecemlineatus	ENSSTOG00000002506	1 retrocopy	retro_itri_1286,
Tarsius syrichta	ENSTSYG00000009806	1 retrocopy	retro_tsyr_1923,
Tursiops truncatus	ENSTTRG00000009867	1 retrocopy	retro_ttru_162,