RetrogeneDB ID: retro_ocun_1522

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:90328952..90329540(-)
• Located in intron of: ENSOCUG00000015851

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYF2
• Ensembl ID: ENSOCUG00000013050
• Aliases: None
• Description: SYF2 homolog, RNA splicing factor (S. cerevisiae) [Source:HGNC Symbol;Acc:19824]

Sequence

>retro_ocun_1522
CAGAATGAAGCTCGTAAATTAAATCACCAGGAAGTTGTGGAAGAAGATAAAAGACTTAAGTTACTGGCAAACTGGGAAGC
CAAGAAAGCTCGTTTGGAATGGAAACTTCAGGAAGAAGAAAAGAAAGAGGAATGTGCAGCCAGAGGGAAAGACTCTGAGA
AATGAAGCTGCTGGAGACCAGCGCAGAGGATGCAGAAAGATGGGAGGAAAAAGAGGAAAACCCCCATCCTGCATTTTCAG
ACTATGCTGACGCCCAGCTACGCCAGTATCACAGGTTGACCCTAGCAGATCAAACCTGACATGGACACGTATGAGAGACT
GAGGGAGAAGCATGGAGAAGAGCTTTTCCCGACATCCAACAGTCTTCTGCAAGGCACACACATGCCCTCTACAGAGATCA
ACAGGATGGTCACCGAGCTGGCAAAGCGAATTGAACCGCGAGACAAACACACGCGGAGGCATCCTTATAACGATGATGTA
GATTTGACTGCATTAATGAGAGAAATGCCAAATTCGCAAGAAAGCTGAAAGGTTCTATAGAAGTACACTGCTGAAATTAA
ATAGAATTTGGAAAGAGGAACAGCTGTT

Alignment

ORF - retro_ocun_1522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.02 %
• Parental protein coverage: 81.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RNEARKLNHQEVVEEDKRLKLPANWEAKKARLEWELQEEEKKKECAARGEDYEK-VKLLEISAEDAERWE
          .NEARKLNHQEVVEEDKRLKL.ANWEAKKARLEW.LQEEEKK.ECAARG.D.EK..KLLE.SAEDAERWE
Retrocopy QNEARKLNHQEVVEEDKRLKLLANWEAKKARLEWKLQEEEKKEECAARGKDSEK<MKLLETSAEDAERWE

Parental  RKKKRKNPDLGFSDYAAAQLRQYHRLTK-QIKPDMETYERLREKHGEEFFPTSNSLLHGTHVPSAEEIDR
          ...K..NP...FSDYA.AQLRQYHRLT..QIKPDM.TYERLREKHGEE.FPTSNSLL.GTH.PS..EI.R
Retrocopy --EKEENPHPAFSDYADAQLRQYHRLTL>QIKPDMDTYERLREKHGEELFPTSNSLLQGTHMPST-EINR

Parental  MVTDLEKQIEKRDKYSRRRPYNDDADI-DYINERNAKF-NKKAERFYG-KYTAEIKQNLERGTAV
          MVT.L.K.IE.RDK..RR.PYNDD.D..D.INERNAKF..KKAERFY..KYTAEIK.NLERGTAV
Retrocopy MVTELAKRIEPRDKHTRRHPYNDDVDL<DCINERNAKF<RKKAERFYR<KYTAEIK*NLERGTAV

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	0.06 RPM	27.32 RPM
SRP017611_kidney	0.00 RPM	38.92 RPM
SRP017611_liver	0.00 RPM	15.95 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1522 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1522 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010115	1 retrocopy	retro_amel_566,
Bos taurus	ENSBTAG00000001651	1 retrocopy	retro_btau_478,
Choloepus hoffmanni	ENSCHOG00000005273	1 retrocopy	retro_chof_2034,
Callithrix jacchus	ENSCJAG00000018559	1 retrocopy	retro_cjac_467,
Homo sapiens	ENSG00000117614	1 retrocopy	retro_hsap_4152,
Monodelphis domestica	ENSMODG00000013951	1 retrocopy	retro_mdom_899,
Oryctolagus cuniculus	ENSOCUG00000013050	1 retrocopy	retro_ocun_1522 ,
Sarcophilus harrisii	ENSSHAG00000007152	1 retrocopy	retro_shar_15,