RetrogeneDB ID: retro_ecab_1096

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:5395748..5396693(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000015264
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AZIN1
• Ensembl ID: ENSECAG00000016922
• Aliases: None
• Description: antizyme inhibitor 1 [Source:HGNC Symbol;Acc:16432]

Sequence

>retro_ecab_1096
GACAGTGAAGTTGAATTGAAGAAAATTGCACGTAATCACCCAAATGCCAAGGTCTTACTACGTTTTGCAACAGAAGATAA
TATTGGAGATGAAGAGGGTAACGTGAAGTTTGGCACTACCCCGAAGAACTGTAGGCATCTCTTGGAATGTGCTAAGGAAC
TTGGTGTCCAAATTATTGGGGTTAAATTTCATGTTTCAAGTGCTTGCAAAGAATCTCAAGCACATGTACATGCTCTGTCT
GATGCTCGATGTATGTTTGACATGGCTGGAGAATTTGGCCTCACAATGAACATGTTAGACATTGGTGGAGGCTTCACAGG
AACTGCATTTCAGTTGGAAGAGGTTAATCATGTTATCAGCCCTGTGTTGGATGTCTACTTTCCTGAAGGATCTGGCATTA
AGATAATTTCAGAACCTGGAAGCTACTATGTGTCTTCTGCATTTACACTTGCAGTTAATATCATTGCGAAGAAAGTTGTT
GAAAATGATAAATTATCCTGTGGAGTAGAAAAAACCAGAAGTGATGAGCCAGCCTTCATGTATTTCATGAACGGTGGTGT
TTATGGTTCTTTTGCAAGTAAACTGTTTGAGGACTTAAATACCTTTCCAGAGGTTCCCAAGAAATACAAGCAAGATGAGC
CTCTGTTTACAAGCAGCCTTTGGGGTCCATCCTGTGATGAGCTTGATCAAATTATGGAAAACTGTCTTCTTCCTGAGCTG
AATGAGGGAGATTGGCTTATCTTTGATAACATGGGAGCAGATTCTTTCCATGACCCATCTGCTTTTAATGATTTTCAGAG
GCCAGCTATTTATTACATGATGTCATTTAGTAATTGGTCTGAGATGCAAGATGCTGGGGTTACTTCAGACACAATGATGA
AGAACTTCTTCTTTGTGCCTTCTTGCATTCCGCTGAGCCAAGAAGACAGCTTTTCCACTGAAGCT

Alignment

ORF - retro_ecab_1096 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.96 %
• Parental protein coverage: 70.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DNEVELKKIARNHPNAKVLLHIATEDNIGGEEGNMKFGTTLKNCRHLLECAKELDVQIIGVKFHVSSACK
          D.EVELKKIARNHPNAKVLL..ATEDNIG.EEGN.KFGTT.KNCRHLLECAKEL.VQIIGVKFHVSSACK
Retrocopy DSEVELKKIARNHPNAKVLLRFATEDNIGDEEGNVKFGTTPKNCRHLLECAKELGVQIIGVKFHVSSACK

Parental  ESQAYVHALSDARCVFDMAGEFGFTMNMLDIGGGFTGTEFQLEEVNHVISPLLDIYFPEESGIKIISEPG
          ESQA.VHALSDARC.FDMAGEFG.TMNMLDIGGGFTGT.FQLEEVNHVISP.LD.YFPE.SGIKIISEPG
Retrocopy ESQAHVHALSDARCMFDMAGEFGLTMNMLDIGGGFTGTAFQLEEVNHVISPVLDVYFPEGSGIKIISEPG

Parental  SYYVSSAFTLAVNIVAKKVVENDKLCSGVEKTGSDEPAFMYYMNDGVYG-FASKLSEDLNTFPEVHKAKK
          SYYVSSAFTLAVNI.AKKVVENDKL..GVEKT.SDEPAFMY.MN.GVYG.FASKL.EDLNTFPEV...KK
Retrocopy SYYVSSAFTLAVNIIAKKVVENDKLSCGVEKTRSDEPAFMYFMNGGVYGSFASKLFEDLNTFPEV--PKK

Parental  YKEDEPLFTSSLWGPSCDELDQIVENCLLPELNVGDWLIFDNMGADSFHEPSAFNDFQRPAVYYMMSFSD
          YK.DEPLFTSSLWGPSCDELDQI.ENCLLPELN.GDWLIFDNMGADSFH.PSAFNDFQRPA.YYMMSFS.
Retrocopy YKQDEPLFTSSLWGPSCDELDQIMENCLLPELNEGDWLIFDNMGADSFHDPSAFNDFQRPAIYYMMSFSN

Parental  WYEMQDAGITSDTMMKNYFFVPSCIQLSQEDSFSTEA
          W.EMQDAG.TSDTMMKN.FFVPSCI.LSQEDSFSTEA
Retrocopy WSEMQDAGVTSDTMMKNFFFVPSCIPLSQEDSFSTEA

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	0.53 RPM	25.32 RPM
SRP021940_cerebellum	0.78 RPM	43.31 RPM
SRP021940_embryo	0.28 RPM	28.72 RPM
SRP021940_placental_villous	1.44 RPM	61.68 RPM
SRP021940_synovial_membrane	0.36 RPM	17.57 RPM
SRP021940_testis	0.77 RPM	26.79 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1096 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1096 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1096 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005164	2 retrocopies	retro_chof_1086, retro_chof_1522,
Equus caballus	ENSECAG00000016922	1 retrocopy	retro_ecab_1096 ,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002, retro_ecab_957,
Oryctolagus cuniculus	ENSOCUG00000015196	1 retrocopy	retro_ocun_1439,
Tursiops truncatus	ENSTTRG00000000140	1 retrocopy	retro_ttru_1210,