RetrogeneDB ID: retro_ocun_1909

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:108595149..108595541(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED4
• Ensembl ID: ENSOCUG00000003964
• Aliases: None
• Description: transmembrane emp24 protein transport domain containing 4 [Source:HGNC Symbol;Acc:22301]

Sequence

>retro_ocun_1909
GGCTCCAAGGGCCGCCTCATAGTCACCTGCCACACACCCGGGACCCTCCGATCTGCCTGTGTTCCAGCTCCACCAGGGAT
GCCTTTCTTTGCTGGTGGCAAGCTGCGTGTGCACCTGGACATGCAGGTTGGGGAGCAGGCCAATAATTACCCTGTGATTG
CTTCCAGGGATAAGCTGACGGAGCAACATCTGCGTGCCCACTAAGCATTGAGCAGTTGGAACAGGTGCAGAAGGAGCAGG
ATTGCCAAAGGTATTGTGAAGAGCCCTTCTGCCTGACCAGCGAGAGCAGCAGCCAGAGAGTCCTGTGATGGTGCATCGTT
CGGACTGTCATCCTCACTGGCATCGGGCAGATGTGTCTCCTCAAGAGCTTCTTTGAAGCCAACAAGCTGGTA

Alignment

ORF - retro_ocun_1909 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.38 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSEGRFTFTSHTPG-DHQICLHSNSTR-MAFFAGGKLRVHLDIQVGEHANNYPEIAAKDKLTELQLRARQ
          GS.GR...T.HTPG.D..ICL.S.STR.M.FFAGGKLRVHLD.QVGE.ANNYP.IA..DKLTE..LRA..
Retrocopy GSKGRLIVTCHTPG<DPPICLCSSSTR>MPFFAGGKLRVHLDMQVGEQANNYPVIASRDKLTEQHLRAH*

Parental  LL-DQVEQIQKEQDYQRYREERFRLTSESTNQRVLWWSIAQTVILILTGIWQMRHLKGFFEAKKLV
          .L..Q.EQ.QKEQD.QRY.EE.F.LTSES..QRVL.W.I..TV..ILTGI.QM..LK.FFEA.KLV
Retrocopy AL<EQLEQVQKEQDCQRYCEEPFCLTSESSSQRVL*WCIVRTV--ILTGIGQMCLLKSFFEANKLV

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	0.17 RPM	34.38 RPM
SRP017611_kidney	0.00 RPM	44.29 RPM
SRP017611_liver	0.00 RPM	14.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1909 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1909 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1909 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
Erinaceus europaeus	ENSEEUG00000007627	2 retrocopies	retro_eeur_12, retro_eeur_317,
Macropus eugenii	ENSMEUG00000006810	1 retrocopy	retro_meug_1225,
Monodelphis domestica	ENSMODG00000016129	2 retrocopies	retro_mdom_256, retro_mdom_362,
Oryctolagus cuniculus	ENSOCUG00000003964	1 retrocopy	retro_ocun_1909 ,
Ictidomys tridecemlineatus	ENSSTOG00000014658	1 retrocopy	retro_itri_1499,