RetrogeneDB ID: retro_ocun_822

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:21323958..21324442(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HTATIP2
• Ensembl ID: ENSOCUG00000000749
• Aliases: None
• Description: HIV-1 Tat interactive protein 2, 30kDa [Source:HGNC Symbol;Acc:16637]

Sequence

>retro_ocun_822
GAAACTGTTTTCCAGAGTCACCCTTACATTGGCCAGAGCGATCTCACTGTTCCTGCGGAAGCTTATAAAAATGTGAATCA
AGAAGTGGTGGACTTTGACATGCTGGATGCCTATGCTTCTGCCTTTCAAGGCCATGATGGTGGGTTCTGTTGCCTGGTAA
CCACTAGAAAAAAAAAACAAGGAGGAGGGATTTTTTCATATTAACAGAGATTATGTGCTGAAGTCTGCAGAGGTGACAAA
AGAAGGAGAGTGCAAACATTTCAACTTGCTTTCCTCTAAAGGAGCTGATAAGTCAAGCAATTTTTTATATCCACAAGTTA
AGAGGGAAGTGGAAGCCATAGTTGAAGAATTAACATCTGGTCATTACTCAATATTTAGGCCCAGAGTTCTATTATGTGAC
AGGCAAGAGTCTTGCCCAGGTGAATAGATGGTTATGGAATTCTTTGGTTCTTTACCAGACTCCTGGGCTGGCGGGCAATC
TGTA

Alignment

ORF - retro_ocun_822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.6 %
• Parental protein coverage: 57.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QRLFSRVTLIGRRKLTFDEEAYKNVNQEVVDFEKLDDYAAAFQGHDVGFCCLGTTRKKAGA-EGFVRVDR
          ...F.....IG...LT...EAYKNVNQEVVDF..LD.YA.AFQGHD.GFCCL.TTRKK....EGF....R
Retrocopy ETVFQSHPYIGQSDLTVPAEAYKNVNQEVVDFDMLDAYASAFQGHDGGFCCLVTTRKKKQG>EGFFHINR

Parental  DYVLKSAELAKAGGCKHFNLLSSKGADKSSNFLYLQVKGEVEARVEELNFDRYSIFRPGVLLCDRQESRP
          DYVLKSAE..K.G.CKHFNLLSSKGADKSSNFLY.QVK.EVEA.VEEL....YSIFRP.VLLCDRQES.P
Retrocopy DYVLKSAEVTKEGECKHFNLLSSKGADKSSNFLYPQVKREVEAIVEELTSGHYSIFRPRVLLCDRQESCP

Parental  GEWMVRKFFGSLPESWARGQSV
          GE.MV..FFGSLP.SWA.GQSV
Retrocopy GE*MVMEFFGSLPDSWAGGQSV

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
SRP017611_brain	0.00 RPM	21.36 RPM
SRP017611_kidney	0.00 RPM	19.66 RPM
SRP017611_liver	0.00 RPM	23.43 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_822 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_822 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_822 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006718	1 retrocopy	retro_cjac_967,
Loxodonta africana	ENSLAFG00000018703	1 retrocopy	retro_lafr_244,
Oryctolagus cuniculus	ENSOCUG00000000749	1 retrocopy	retro_ocun_822 ,
Pongo abelii	ENSPPYG00000003421	1 retrocopy	retro_pabe_1288,
Ictidomys tridecemlineatus	ENSSTOG00000011216	2 retrocopies	retro_itri_1354, retro_itri_1523,