RetrogeneDB ID: retro_ocun_1786

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018889:475611..476256(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021804
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GCA
• Ensembl ID: ENSOCUG00000002868
• Aliases: None
• Description: grancalcin, EF-hand calcium binding protein [Source:HGNC Symbol;Acc:15990]

Sequence

>retro_ocun_1786
ATGGCCTACCCAGGATACGAAGGAGGGTTTGGAAATTTTAGTAGTCAGATGCCAGGGATGCAGCCAATGCCAGGGGCAGG
TCCAAACGTGTTCCTTGGTGGGTACCCCGGACCCCTGCCTTATTCAGACAGTTACTCTTCAGCTGGGGACCCCATGTGGA
GTTACTTCACAGCTGTTGCTGGACAGGATGGTGAAGTGGATGCTGAAGAACTTCAGAGATGTTTGACAGAGTCTGGAATT
AGTGGAACTTATTCTCCCTTCAGTTTGGAAACATGCAGAATTATGATTGCCATGTTGGATAGAGATTATACAGGAAAAAT
GGGATTTAATGAATTCAAGGAGCTTTGGGCAGCTCTTACTGCATGGAAGGAAAACTTCATAACTATTGATCGAGACCGAA
GTGGCACAGTAGAGCATCACGAGTTGAGTCAATCCATTGCTATTATGGGTTATAGGTTGAGTCCTCAGACGTTAAATACT
ATTGTTAGACGCTACAGTAAGAATGGCAGAATTTTCTTTGATGATTATGTTGCTTGTTGTGTGAAGCTTCATGCCTTGAC
AGATTTCTTTAGGAGAAGAGACCACTTGCAACAAGGATTTGTGAATTTCGTGTATGATGATTTTTTGCAGGGCACTATGG
CAATC

Alignment

ORF - retro_ocun_1786 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAYPGYGGGFGNFSGQMPGMQPMPGAGPNVFLGGYPGPLPYSDSYSSAGDPMWSYFTAVAGQDGEVDAEE
          MAYPGY.GGFGNFS.QMPGMQPMPGAGPNVFLGGYPGPLPYSDSYSSAGDPMWSYFTAVAGQDGEVDAEE
Retrocopy MAYPGYEGGFGNFSSQMPGMQPMPGAGPNVFLGGYPGPLPYSDSYSSAGDPMWSYFTAVAGQDGEVDAEE

Parental  LQRCLTESGISGTYSPFSLETCRIMIAMLDRDYTGKMGFNEFKELWAALTAWKENFMTIDRDRSGTVEHH
          LQRCLTESGISGTYSPFSLETCRIMIAMLDRDYTGKMGFNEFKELWAALTAWKENF.TIDRDRSGTVEHH
Retrocopy LQRCLTESGISGTYSPFSLETCRIMIAMLDRDYTGKMGFNEFKELWAALTAWKENFITIDRDRSGTVEHH

Parental  ELSQSIAIMGYRLSPQTLNTIVRRYSKNGRIFFDDYVACCVKLRALTDFFRRRDHLQQGFVNFVYDDFLQ
          ELSQSIAIMGYRLSPQTLNTIVRRYSKNGRIFFDDYVACCVKL.ALTDFFRRRDHLQQGFVNFVYDDFLQ
Retrocopy ELSQSIAIMGYRLSPQTLNTIVRRYSKNGRIFFDDYVACCVKLHALTDFFRRRDHLQQGFVNFVYDDFLQ

Parental  GTMAI
          GTMAI
Retrocopy GTMAI

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	0.22 RPM	11.31 RPM
SRP017611_kidney	0.00 RPM	2.74 RPM
SRP017611_liver	0.00 RPM	0.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1786 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1786 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1786 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006229	2 retrocopies	retro_chof_2009, retro_chof_34,
Dasypus novemcinctus	ENSDNOG00000012124	1 retrocopy	retro_dnov_1114,
Oryctolagus cuniculus	ENSOCUG00000002868	2 retrocopies	retro_ocun_1786 , retro_ocun_741,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,