RetrogeneDB ID: retro_ocun_383

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:105952669..105953146(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF1
• Ensembl ID: ENSOCUG00000017023
• Aliases: None
• Description: activating transcription factor 1 [Source:HGNC Symbol;Acc:783]

Sequence

>retro_ocun_383
GATGGAGCCTTACAGTTGGCCAGTCCAGGCGCAGACGGAGTACAGGGACTGCAGACGTTGCCCATGACCAATTCAGGCAG
CACTCAGCAAGGTACAATTCTGCAGTAGGCACAGACCTCGGAAGGACAGCAAATACTTGTGCCCAGCAACCAGGTGGTTG
TACAGACAGCCTCAGGAGATATGCAGACCTACCAGATCCGGACCACGCCCTCGGCGACTTCACTGCCACAGGCTGTGGTG
ATGACGTCTCCTGTGACGCTGACGTCTCAGACAACTAAGACAGATGACTAAGATGACCCTCAGTTGAAGAGAGAAATACG
GCTCACGAAAAACAGAGAAGCTGCTCGAGAATGTCGCAGAAAGAAGAAAGAGTATGTGAAATGCCTGGAGAATCGAGTTG
CAGTTCTAGAGAATCAAAATAAAACTCTGATAGAAGAGTTAAAGACTTTAAAAGATCTTTATTCCCATAAAAGTGTT

Alignment

ORF - retro_ocun_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.79 %
• Parental protein coverage: 58.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGALQLASPGADGVQGLQTLPMTNSGSTQQGTILQYAQTSDGQQILVPSNQVVVQT-SGDMQTYQIRTTP
          .GALQLASPGADGVQGLQTLPMTNSGSTQQGTILQ.AQTS.GQQILVPSNQVVVQT.SGDMQTYQIRTTP
Retrocopy DGALQLASPGADGVQGLQTLPMTNSGSTQQGTILQ*AQTSEGQQILVPSNQVVVQTASGDMQTYQIRTTP

Parental  SATSLPQAVVMTSPVTLTSQTTKT---DDPQLKREIRLMKNREAARECRRKKKEYVKCLENRVAVLENQN
          SATSLPQ.............TTKT...DDPQLKREIRL.KNREAARECRRKKKEYVKCLENRVAVLENQN
Retrocopy SATSLPQXXXXXXXXXXXXXTTKTDD*DDPQLKREIRLTKNREAARECRRKKKEYVKCLENRVAVLENQN

Parental  KTLIEELKTLKDLYSHKSV
          KTLIEELKTLKDLYSHKSV
Retrocopy KTLIEELKTLKDLYSHKSV

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	1.71 RPM	12.91 RPM
SRP017611_kidney	2.33 RPM	21.39 RPM
SRP017611_liver	1.39 RPM	14.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_383 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_383 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004733	5 retrocopies	retro_chof_1987, retro_chof_2305, retro_chof_27, retro_chof_462, retro_chof_760,
Erinaceus europaeus	ENSEEUG00000008000	2 retrocopies	retro_eeur_332, retro_eeur_704,
Homo sapiens	ENSG00000123268	1 retrocopy	retro_hsap_3633,
Mus musculus	ENSMUSG00000023027	1 retrocopy	retro_mmus_3609,
Oryctolagus cuniculus	ENSOCUG00000017023	1 retrocopy	retro_ocun_383 ,
Otolemur garnettii	ENSOGAG00000026029	1 retrocopy	retro_ogar_1378,
Procavia capensis	ENSPCAG00000010038	2 retrocopies	retro_pcap_303, retro_pcap_442,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635,