RetrogeneDB ID: retro_ocun_1190

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:45430127..45431402(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLA
• Ensembl ID: ENSOCUG00000010859
• Aliases: None
• Description: galactosidase, alpha [Source:HGNC Symbol;Acc:4296]

Sequence

>retro_ocun_1190
ATGAAGTCGGGAGGCGGAAGTCAGTGGCGGGGTTGCTTGCTTGCACTTCGCTTCCTCTTCCTATTTTTCTGGGGCGTCCC
TGGGGCCAGGGCATTGGACAATGGCTTGGCGAGGACGCCTACCATGGGCTGGCTACACTGGGAGCGCTTCCTATGTAATC
TTGACTGCCAGGCAGAGCCGGAATCCTGCATCAGTGAGCATCTCTTCATGCAGATGGCAGAGCTCATGGTCTCAGATGGC
TGGAAGGATGCCGGTTATGAATGCCTCTGCATTGACGACTGTTGGATGGCTCCCGAAAGAGATCCAAAAGGCAGGCTTCA
GGCGGACCCTCAGCGCTTTCCTGGGGGGATCCGCCGCCTTGCTGATTATGTCCACAGCAAAGGACTAAAGCTAGGGATTT
ATGCAGATGTTGGAAATAAAACCTGTGCAGGGTACCCTGGGAGTTTCGGACACTATGACATTGATGCCCAGACCTTTGCT
GACTGGGGAGTAGATCTGCTAAAATTTGATGGTTGTCACTGTGACAGTGTGAAGCATTTGATTGAAGGTTATCAGTACAT
GTCCTTGGCTCTGAACAGGACTGGCAGAAGCATTGTATACTCCTGTGAGTGGCCTCTTTATATGTGGCCCTTTCATAAGC
CCAATTACACAAAAATTCGGACATACTGCAATCACTGGAGAAATTCTGCTGACATTTATGATTCCTGGGAAAGTATAAAG
AGTATCTTGGCCTGGACATCTTCTAACCAGGAGAAAATTGTTGATGTTGCTGGACCAGGGGGCTGGAATAACCCAGATAT
GTTAGTGATTGGCAACTTTGGCCTCAGCTGGAATCAACAAGTAACTCAGATGGCTCTCTGGGCTATCATGGCAGCTCCTT
TAATCATGTCTAATGACCTCAGACACATCAGCCCTCAAGCCAAAAGTTTACTTCAGAATAAAGATGTGATTGCCATCAAC
CAGGACCCCTTGGGCAAGCAGGGGTACCTGCTTAGAAAGGAAAGCAGCATTGAGGTGTGGGAATGACCCCTCTCAAACTT
ATCCTGGGCTGTAGCCGTTATGAACCTGCAGGAAATTGGTGGACCCTGTTATTATACCATCGCAGTTGCTTCCCTTGGAA
GATGAATAGCATGTAATCCTGCCTGCCTCATCACACAGCTCCTCCCTGAGAAAAGGAAACTTGGGTTCTATACATGGACT
TCAAGCATAAAAACCCGAGTAAATCCCACAGGCACCGTTTTGCTCCAGCTAGGTGGGACAAGTAAGACTACATCA

Alignment

ORF - retro_ocun_1190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.65 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSGRGRQWRGCLLALRFLFLFFWGVPGARALDNGLARTPTMGWLHWERFLCNLDCQAEPESCISEHLFM
          MKSG.G.QWRGCLLALRFLFLFFWGVPGARALDNGLARTPTMGWLHWERFLCNLDCQAEPESCISEHLFM
Retrocopy MKSGGGSQWRGCLLALRFLFLFFWGVPGARALDNGLARTPTMGWLHWERFLCNLDCQAEPESCISEHLFM

Parental  QMAELMVSDGWKDAGYEYLCIDDCWMAPERDPEGRLQADPQRFPGGIRRLADYVHSKGLKLGIYADVGNK
          QMAELMVSDGWKDAGYE.LCIDDCWMAPERDP.GRLQADPQRFPGGIRRLADYVHSKGLKLGIYADVGNK
Retrocopy QMAELMVSDGWKDAGYECLCIDDCWMAPERDPKGRLQADPQRFPGGIRRLADYVHSKGLKLGIYADVGNK

Parental  TCAGYPGSFGHYDIDAQTFADWGVDLLKFDGCHCDSVKHLIEGYQYMSLALNRTGRSIVYSCEWPLYMWP
          TCAGYPGSFGHYDIDAQTFADWGVDLLKFDGCHCDSVKHLIEGYQYMSLALNRTGRSIVYSCEWPLYMWP
Retrocopy TCAGYPGSFGHYDIDAQTFADWGVDLLKFDGCHCDSVKHLIEGYQYMSLALNRTGRSIVYSCEWPLYMWP

Parental  FHKPNYTKIRTYCNHWRNSADIYDSWESIKSILAWTSSNQEKIVDVAGPGGWNDPDMLVIGNFGLSWNQQ
          FHKPNYTKIRTYCNHWRNSADIYDSWESIKSILAWTSSNQEKIVDVAGPGGWN.PDMLVIGNFGLSWNQQ
Retrocopy FHKPNYTKIRTYCNHWRNSADIYDSWESIKSILAWTSSNQEKIVDVAGPGGWNNPDMLVIGNFGLSWNQQ

Parental  VTQMALWAIMAAPLIMSNDLRHISPQAKSLLQNKDVIAINQDPLGKQGYLLRKESSIEVWERPLSNLSWA
          VTQMALWAIMAAPLIMSNDLRHISPQAKSLLQNKDVIAINQDPLGKQGYLLRKESSIEVWE.PLSNLSWA
Retrocopy VTQMALWAIMAAPLIMSNDLRHISPQAKSLLQNKDVIAINQDPLGKQGYLLRKESSIEVWE*PLSNLSWA

Parental  VAVMNLQEIGGPCYYTIAVASLGRGIACNPACLITQLLPEKRKLGFYTWTSSIKTRVNPTGTVLLQLGGT
          VAVMNLQEIGGPCYYTIAVASLGR.IACNPACLITQLLPEKRKLGFYTWTSSIKTRVNPTGTVLLQLGGT
Retrocopy VAVMNLQEIGGPCYYTIAVASLGR*IACNPACLITQLLPEKRKLGFYTWTSSIKTRVNPTGTVLLQLGGT

Parental  NKSMS
          .K..S
Retrocopy SKTTS

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	2.15 RPM
SRP017611_kidney	1.01 RPM	12.77 RPM
SRP017611_liver	0.08 RPM	2.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1190 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1190 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010267	1 retrocopy	retro_chof_1479,
Monodelphis domestica	ENSMODG00000011590	1 retrocopy	retro_mdom_204,
Oryctolagus cuniculus	ENSOCUG00000010859	1 retrocopy	retro_ocun_1190 ,
Ictidomys tridecemlineatus	ENSSTOG00000004771	1 retrocopy	retro_itri_1519,