RetrogeneDB ID: retro_ocun_1745

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018838:451993..452547(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSOCUG00000004387
• Aliases: None
• Description: RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]

Sequence

>retro_ocun_1745
TCCTCTGGCTCCCTGAGCCCCTCCTGGTGCAGGCACAACAACAGATGGTGCTCACGCTCCAAATCCTAACCCCCTAAAAG
AGATGAAAAGGAGAGGAAAAGACAGAGCCCGTCCCCTAAACCCACCAAAGTGCACACTGGGAGGCTCACCAGGAATGTGA
CCAAGGGCCACATCATGGAGATATTTTCCACCTATGGGAAGATTAAAATGATTGACATGCCTGTCGACAGGATGCACCCC
CACCTGTCCAAAGGCTACAGCTATGTGGAGTTTGAGAACTGGACGAGGCCGAGAAGGCACTGAAGCACATGAACAGAGGA
CAGATCGATGGCCAGGAGATCACTGCTACTGCTGTGCTGACCCCCTGGCCCCAGCCGCCCCCTCGGTGATTCAGTCCTCC
CAGGAGAATGCTCCCACCACCTCCTATGTGACACCGGTCACCCCCGCGAATGTGGAGAAGGTCTCGCTCCCCGAGGTGCA
GGCCTCCCATGCGCCGGCGATCCTGGTCTCCCGGCAGCCACCGCCACAGGAGCCGCTCCAGCTCCAACTCTTCC

Alignment

ORF - retro_ocun_1745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 60.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSGSPSPSRRRHDNRRRSRSKSKPPKRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKM
          SSGS.SPS..RH.NR..SRSKS.PPKRDEKERKR.SPSPKPTKVH.GRLTRNVTK.HIMEIFSTYGKIKM
Retrocopy SSGSLSPSWCRHNNRWCSRSKS*PPKRDEKERKRQSPSPKPTKVHTGRLTRNVTKGHIMEIFSTYGKIKM

Parental  IDMPVDRMHPHLSKGYAYVEFEN-PDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLP
          IDMPVDRMHPHLSKGY.YVEFEN..DEAEKALKHM..GQIDGQEITATAVL.PWP.PPPR.FSPPRRMLP
Retrocopy IDMPVDRMHPHLSKGYSYVEFEN<LDEAEKALKHMNRGQIDGQEITATAVLTPWPQPPPR*FSPPRRMLP

Parental  PPPMWRRSPPRMRRRSRSPRRRSPVRRRSRSPGRRRHRSRSSSNSS
          PPPM..RSPPRM.RRSRSPR.R.P.RRRS.SPG..RHRSRSSSNSS
Retrocopy PPPM*HRSPPRMWRRSRSPRCRPPMRRRSWSPGSHRHRSRSSSNSS

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	0.11 RPM	96.91 RPM
SRP017611_kidney	0.00 RPM	79.87 RPM
SRP017611_liver	0.31 RPM	27.59 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1745 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1745 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1745 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014969	2 retrocopies	retro_cjac_2127, retro_cjac_3377,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Myotis lucifugus	ENSMLUG00000016808	3 retrocopies	retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Mus musculus	ENSMUSG00000034681	1 retrocopy	retro_mmus_173,
Oryctolagus cuniculus	ENSOCUG00000004387	2 retrocopies	retro_ocun_1544, retro_ocun_1745 ,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,