RetrogeneDB ID: retro_ocun_1041

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:47435960..47436656(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERBP1
• Ensembl ID: ENSOCUG00000008946
• Aliases: None
• Description: SERPINE1 mRNA binding protein 1 [Source:HGNC Symbol;Acc:17860]

Sequence

>retro_ocun_1041
ATGCCTGGGCACCTACAGGAAGGCTTCGGCTGCGTGGTCACCAACCGATTCGACCAGTTATTTGACGACGAATCGGACCC
CTTCGAGGTGCTGAAGGCAGCAGAGAACAAGAAAAAAGAAGCCGGCGGGGGCGGCGTTGGGGGCCCCGGGGCCAAGAGCG
CAGCTCAGGCCGCGGCCCAGACCAACTCCAACGCGGCAGGCAAACAGCTGCGTAAAGAGTCCCAGAAAGACCGCAAAAAC
CCGCTGCCTCCCAACGTTGGCGTGGTTGACAAGAAAGAGGAGACGCAGCCGCCCGTGGCGCTCAAGAAAGAAGGAATAAG
ACGTGTTGGGAGAAGACCTGATCAACAACTTCAAGGTGAAGGGAAAATAATTGATAGAAGACCAGAAAGGCGACCACCTC
GTGAAAGAAGATTTGAAAAGCTACTAGAAGAAAAGGGTGAAGGAGGAGAGTTTTCAGTTGATAGGCCTATAATTGACCGA
CCTATCCGAGGCCATGGTGGTCTTGGAAGAGGTCAAGGAGGCCGTGGACGTGGAATGGGCTGAGGAGATGGATTTGATTC
TCGTGGCAAACGTGAATTTGACAGGCATAGTGGAAGTGATAGATCTTTTTCACATTACAGTGGTCTGAAGCACGAGGACA
AACGTGGAGGTAGCGGATCTCACAACTGGGGAACTGTCAAAGATGAATTAACTGAC

Alignment

ORF - retro_ocun_1041 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 57.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGGGGVGGPGAKSAAQAAAQTNSNAAGKQL
          MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGGGGVGGPGAKSAAQAAAQTNSNAAGKQL
Retrocopy MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGGGGVGGPGAKSAAQAAAQTNSNAAGKQL

Parental  RKESQKDRKNPLPPNVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQGEGKIIDRRPERRPPRERRFEK
          RKESQKDRKNPLPPNVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQGEGKIIDRRPERRPPRERRFEK
Retrocopy RKESQKDRKNPLPPNVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQGEGKIIDRRPERRPPRERRFEK

Parental  PLEEKGEGGEFSVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGL
          .LEEKGEGGEFSVDRPIIDRPIRG.GGLGRG.GGRGRGMG.GDGFDSRGKREFDRHSGSDR.SFSHYSGL
Retrocopy LLEEKGEGGEFSVDRPIIDRPIRGHGGLGRGQGGRGRGMG*GDGFDSRGKREFDRHSGSDR-SFSHYSGL

Parental  KHEDKRGGSGSHNWGTVKDELTE
          KHEDKRGGSGSHNWGTVKDELT.
Retrocopy KHEDKRGGSGSHNWGTVKDELTD

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	5.02 RPM	46.74 RPM
SRP017611_kidney	8.41 RPM	49.66 RPM
SRP017611_liver	3.70 RPM	28.59 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1041 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1041 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1041 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017440	2 retrocopies	retro_cjac_1207, retro_cjac_3015,
Gorilla gorilla	ENSGGOG00000010396	1 retrocopy	retro_ggor_408,
Myotis lucifugus	ENSMLUG00000001424	1 retrocopy	retro_mluc_691,
Oryctolagus cuniculus	ENSOCUG00000008946	1 retrocopy	retro_ocun_1041 ,
Pongo abelii	ENSPPYG00000001256	1 retrocopy	retro_pabe_3790,
Sorex araneus	ENSSARG00000000803	1 retrocopy	retro_sara_135,
Tupaia belangeri	ENSTBEG00000003689	4 retrocopies	retro_tbel_1004, retro_tbel_1331, retro_tbel_2427, retro_tbel_532,