RetrogeneDB ID: retro_ocun_1080

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:546853..547398(-)
• Located in intron of: ENSOCUG00000011611

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000013866
• Aliases: None
• Description: selenoprotein T (SELT), mRNA [Source:RefSeq mRNA;Acc:NM_001199819]

Sequence

>retro_ocun_1080
GCAGTGACCCAGAGCAAGGCCTCAGCCAACCTGGGCAGTGTGCCAAGCAAGAGATTAAAGATGCAGTACGCTACGGGGCT
GCTGCTTAAGTTCCAGATCTGTGTTTCCTGAAGGTATAGGCGGGTGTTTGAGGAGTACATGTGGGCTATTAGCCAGCGGT
ACCCAGACAGCCGAATTGAAGGAGAGAATTACCTCCCTCAACCAATATATAGACACATAGCATCTTTCCTGTCAGTCTTC
AAACTATTAATAGGCTGAATAATTGTTGGCAAAGATCCTTTTGCTTTCTTTGGCATGCAAGCTCCTAGCATCTGGTTTGG
GGCCAGGAAAATAAGGTCTATGCATGTGTGATGGTTTTCTTCTTGAGCAACATGATTGAGAACCAGTGTATGTCGACAGG
TGCACTTGAGAGAACTTTAAATGATGTACCTGTGTGGTCTAAACTGGAATCTGGTCACCTTCCATCCATGCAACAACTTG
TTCACATTCTTGACAGTGAAATGAAACTCAGTGTGCATATGGATTCAATCCCACACCGTCAGTCA

Alignment

ORF - retro_ocun_1080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.63 %
• Parental protein coverage: 93.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVARSEASANLGGVPSKRLKMQYATGPLLKFQICVAVSCRYRRVFEEYMRVISQRYPDIRIEGENYLPQP
          AV..S.ASANLG.VPSKRLKMQYATG.LLKFQICV..S.RYRRVFEEYM..ISQRYPD.RIEGENYLPQP
Retrocopy AVTQSKASANLGSVPSKRLKMQYATGLLLKFQICV--S*RYRRVFEEYMWAISQRYPDSRIEGENYLPQP

Parental  IYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIW-QWGQENKVYACMMVFFLSNMIENQCMSTGAF
          IYRHIASFLSVFKL.LIG.IIVGKDPFAFFGMQAPSIW..WGQENKVYAC.MVFFLSNMIENQCMSTGA.
Retrocopy IYRHIASFLSVFKL-LIG*IIVGKDPFAFFGMQAPSIW<VWGQENKVYACVMVFFLSNMIENQCMSTGAL

Parental  EITLNDVPVWSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHRS
          E.TLNDVPVWSKLESGHLPSMQQLV.ILD.EMKL.VHMDSIPH..S
Retrocopy ERTLNDVPVWSKLESGHLPSMQQLVHILDSEMKLSVHMDSIPHRQS

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	37.91 RPM
SRP017611_kidney	0.00 RPM	58.08 RPM
SRP017611_liver	0.00 RPM	9.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1080 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1080 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002576	1 retrocopy	retro_cpor_459,
Erinaceus europaeus	ENSEEUG00000013363	2 retrocopies	retro_eeur_63, retro_eeur_697,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Oryctolagus cuniculus	ENSOCUG00000013866	9 retrocopies	retro_ocun_1080 , retro_ocun_1229, retro_ocun_1783, retro_ocun_1803, retro_ocun_1831, retro_ocun_327, retro_ocun_328, retro_ocun_557, retro_ocun_779,
Pongo abelii	ENSPPYG00000029483	1 retrocopy	retro_pabe_3478,
Tursiops truncatus	ENSTTRG00000007522	2 retrocopies	retro_ttru_1556, retro_ttru_694,