RetrogeneDB ID: retro_ocun_680

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:5203740..5205399(+)
• Located in intron of: ENSOCUG00000016348

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLYR1
• Ensembl ID: ENSOCUG00000010486
• Aliases: None
• Description: glyoxylate reductase 1 homolog (Arabidopsis) [Source:HGNC Symbol;Acc:24434]

Sequence

>retro_ocun_680
ATGGCGACTGTGAGTCTGCGGCTCGGCGACTTGGTGTGGGGGAAGCTCGGCCGGTACCCTCCTTGGCCTGGGAAGATTGT
TAATCCACCCAAAGACTTGAAGAAACCACGTGGAAAGAAATGCTTCTTTGTGAAGTTTTTCGGAACAGAAGATCATGCTT
GGATTAAAGTGGAGCAGCTCAAGCCATATCATGCTCACAAGGAGGAGATGATCAAGATTAACAAGGGCAAGCGGTTCCAA
CAGGCTGTGGATGCCGTGGAAGAGTTCCTCAGGAGAGCCAAGGGGAAAGACCAGACCTCATCCCACAGTTCTGCTGATGA
CAAGAATCGGTGTAATTCCAGTGAGGAAAGAAGTAGGCCAAACTCAGGTGATGAGAAGCGCAAACTTAGCCTGTCTGAAG
GGAAGGTGAAGAAGAACATGGGAGAAGGAAAGAAGAGGGTGTCTTCAGGCTCTGCAGAGAGAGGCTCCAAATCCCCCCTG
AAAAGAGCCCAAGAGCAAAGTCCCCGGAAGCGGGGTCGGCCCCCAAAGGATGAGAAGGATCTCACCATCCCCGCGTCTAG
TACCGTGAAGGGGATGATGGCTGGACCGATGGCCGCGTTTAAATGGCAGCCGACCGTGAGTGAGCCCGTTAAAGACGCAG
ATCCTCATTTCCATCACTTCCTGCTGAGCCAGACGGAGAAGCCAGCTGTCTGTTACCAGGCAATCACAAAGAAGTTGAAA
ATATGTGAAGAGGAAACTGGATCCACCTCTATCCAGGCAGCAGACAGCACAGCTGTGAATGGCAGCATCACACCCACAGA
CAAAAAGATAGGATTTTTGGGCCTTGGACTCATGGGAAGTGGCATCATCTCCAACTTACTAAAAATGGGTCACACAGTGA
CTGTCTGGAACCGGACTGCCGAAAAATGTGATTTGTTCATCCAGGAGGGGGCCCGCCTGGGAAGAACCCCCGCTGAAGTT
GTTTCAACTTGTGACATCACTTTCACCTGTGTGTCAGATCCTAAGGCAGCCAAGGACCTGGTGCTGGGCCCCAGCGGTGT
GCTGCAAGGGATCCGCCCGGGGAAGTGCTACGTGGACATGTCAACAGTGGACGCCGACACAGTCACCGAGCTCGCCCAGG
TGATTGTGTCCAGGGGGGGCCGCTTTCTGGAGGCCCCAGTCTCAGGGAACCAGCAGCTGTCTAATGATGAGATGTTGGTG
ATCTTAGCAGCCGAAGACAGGGGCTTGTACGAGGACTGCAGCAGCTGCTTCCAGGCGATGGGGAAGACCTCCTTCTTCCT
AGGTGAAGTTGGCAACGCAGCCAGGATGATGCTGATTGTGAACATGGTCCAGGGGAGCTTCATGGCCACCATTGCTGAGG
GACTGACCCTGGCCCAGGTGACAGGCCAGTCACAACAGACGCTCTTAGACATCCTCAATCAGGGACAGCTGGCCAGCATT
TTCCTGGACCAGAAATGCCAAAATATCCTACAAGGAAACTTTAAGCCTGATTTCTACCTGAAATATATTCAAAAGGATCT
CCGCTTAGCCATTGCACTGGGTGATGCCGTCAACCATCCAACTCCTATGGCAGCTGCAGCCAATGAGGTATACAAAAGAG
CCAAGGCACTGGACCAGTCTGACAACGATATGTCTGCCATGTACCGAGCCTACATCCAC

Alignment

ORF - retro_ocun_680 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATVSLRLGDLVWGKLGRYPPWPGKIVNPPKDLKKPRGKKCFFVKFFGTEDHAWIKVEQLKPYHAHKEEM
          MATVSLRLGDLVWGKLGRYPPWPGKIVNPPKDLKKPRGKKCFFVKFFGTEDHAWIKVEQLKPYHAHKEEM
Retrocopy MATVSLRLGDLVWGKLGRYPPWPGKIVNPPKDLKKPRGKKCFFVKFFGTEDHAWIKVEQLKPYHAHKEEM

Parental  IKINKGKRFQQAVDAVEEFLRRAKGKDQTSSHSSADDKNRRNSSEERSRPNSGDEKRKLSLSEGKVKKNM
          IKINKGKRFQQAVDAVEEFLRRAKGKDQTSSHSSADDKNR.NSSEERSRPNSGDEKRKLSLSEGKVKKNM
Retrocopy IKINKGKRFQQAVDAVEEFLRRAKGKDQTSSHSSADDKNRCNSSEERSRPNSGDEKRKLSLSEGKVKKNM

Parental  GEGKKRVSSGSAERGSKSPLKRAQEQSPRKRGRPPKDEKDLTIPESSTVKGMMAGPMAAFKWQPTVSEPV
          GEGKKRVSSGSAERGSKSPLKRAQEQSPRKRGRPPKDEKDLTIP.SSTVKGMMAGPMAAFKWQPTVSEPV
Retrocopy GEGKKRVSSGSAERGSKSPLKRAQEQSPRKRGRPPKDEKDLTIPASSTVKGMMAGPMAAFKWQPTVSEPV

Parental  KDADPHFHHFLLSQTEKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGLMGS
          KDADPHFHHFLLSQTEKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGLMGS
Retrocopy KDADPHFHHFLLSQTEKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGLMGS

Parental  GIVSNLLKMGHTVTVWNRTAEKCDLFIQEGARLGRTPAEVVSTCDITFACVSDPKAAKDLVLGPSGVLQG
          GI.SNLLKMGHTVTVWNRTAEKCDLFIQEGARLGRTPAEVVSTCDITF.CVSDPKAAKDLVLGPSGVLQG
Retrocopy GIISNLLKMGHTVTVWNRTAEKCDLFIQEGARLGRTPAEVVSTCDITFTCVSDPKAAKDLVLGPSGVLQG

Parental  IRPGKCYVDMSTVDADTVTELAQVIVSRGGRFLEAPVSGNQQLSNDGMLVILAAGDRGLYEDCSSCFQAM
          IRPGKCYVDMSTVDADTVTELAQVIVSRGGRFLEAPVSGNQQLSND.MLVILAA.DRGLYEDCSSCFQAM
Retrocopy IRPGKCYVDMSTVDADTVTELAQVIVSRGGRFLEAPVSGNQQLSNDEMLVILAAEDRGLYEDCSSCFQAM

Parental  GKTSFFLGEVGNAAKMMLIVNMVQGSFMATIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNIL
          GKTSFFLGEVGNAA.MMLIVNMVQGSFMATIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNIL
Retrocopy GKTSFFLGEVGNAARMMLIVNMVQGSFMATIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNIL

Parental  QGNFKPDFYLKYIQKDLRLAIALGDAVNHPTPMAAAANEVYKRAKALDQSDNDMSAVYRAYIH
          QGNFKPDFYLKYIQKDLRLAIALGDAVNHPTPMAAAANEVYKRAKALDQSDNDMSA.YRAYIH
Retrocopy QGNFKPDFYLKYIQKDLRLAIALGDAVNHPTPMAAAANEVYKRAKALDQSDNDMSAMYRAYIH

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	2.54 RPM	52.70 RPM
SRP017611_kidney	3.85 RPM	46.22 RPM
SRP017611_liver	1.00 RPM	17.03 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_680 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_680 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019912	1 retrocopy	retro_cjac_2514,
Erinaceus europaeus	ENSEEUG00000011783	1 retrocopy	retro_eeur_477,
Homo sapiens	ENSG00000140632	1 retrocopy	retro_hsap_2432,
Gorilla gorilla	ENSGGOG00000016258	1 retrocopy	retro_ggor_1512,
Macaca mulatta	ENSMMUG00000009567	1 retrocopy	retro_mmul_621,
Nomascus leucogenys	ENSNLEG00000009950	1 retrocopy	retro_nleu_240,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896,
Oryctolagus cuniculus	ENSOCUG00000010486	1 retrocopy	retro_ocun_680 ,
Pongo abelii	ENSPPYG00000007072	1 retrocopy	retro_pabe_1791,
Pan troglodytes	ENSPTRG00000007730	1 retrocopy	retro_ptro_1404,