RetrogeneDB ID: retro_ocun_1903

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:82014896..82016031(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023356
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GALT
• Ensembl ID: ENSOCUG00000024714
• Aliases: None
• Description: galactose-1-phosphate uridylyltransferase [Source:HGNC Symbol;Acc:4135]

Sequence

>retro_ocun_1903
ATGTCGCGCGGCGGAACCGACTCCGAGCAGCGCCAGCAGGCGTCAGAGGCAGACGCCACCAAAACAGCCTTCCTGGCAAG
CGAGCATCAGCATATCCGCTACAACCCGCTGCAGGATGAGTGGGTGCTGGTGTCAGCTCACCGCATGAAGCGGCCCTGGC
AGGGGCAAGTGGAGCCCGAGCCTCTGAAGACAGTGCCCCGCCACGACCCCCTCAACCCTCTGTGTCCCGGGGCCACCCGG
GCCAATGGAGAGGTGAATCCTAACTATGATGGCACCTTCCTGTTCGACAACGACTTCCCAGCTCTGCAGCCTGATGCCCC
TAATCCAGGACCCAGCGATCACCCGCTTTTCCAAGTGCAGGCTGCCCGAGGAGTTTGTAAGGTCATGTGCTTCCACCCCT
GGTCGGATGTGACGCTGCCACTCAATGTCAGTCCCTGAGATCCGGGCTGTCGTCGATGCATGGGCCTCAGTCACAGAGGA
TCTGGGTGCTCAGTACCCTTGGGTGCAGATCTTTGAAAACAAAGGAGCCATGATGGGCTGTTCCAATCCCCACCCCCATT
GCCAGGTGTGGGCCAGCAGCTTCCTGCCAGATATTGCCCAGCGCGAGGAGAGATCTCAGCGGGCCTATCACAGTCAACAC
GGAGAGCCTCTGCTGATGGAGTATGGCCGCCAGGAGCTGCTCCGGAAGGACCATCTGGTCCTAACCAGCGAGCACTGGTT
GGTGCTGGTCCCCTTCTGGGCAGTGTGGACCTTGCAGACACTGCTGCTGCCCCGTCGCCATGTGTGGTGGCTGCCTGAGC
TGACCCCCACTGAGCGCGATGATCTGGCCTCCATCATGAAGAAGCTCTTGACCAAGTACGACAACCTGTTTGAGACTTCC
CTTCCCTACTCCATGGGCTGGCATGGAGCTCCCACAGGGTCAGAGGCTGGGGCCACCTGGGACCACTGGCAGCTGCACGC
TCACTACTACCCTCCACTCCTCCGCTCTGCCACTCACCGCAAATTCATGGTTGGCTATGAAATGCTTACTCAGGCTCAGA
GGGACCTCACTCCTGAGCAGGCTACAGAGAGACTAAGGGCACTTCCTGAGGTTCATTACCGCCTGAGGCAGAAGGACAAG
GAGACTGCGGCCATC

Alignment

ORF - retro_ocun_1903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.04 %
• Parental protein coverage: 99.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSRGGTDSEQRQQASEADATKTAFRASEHQHIRYNPLQDEWVLVSAHRMKRPWQGQVEPEPLKTVPRHDP
          MSRGGTDSEQRQQASEADATKTAF.ASEHQHIRYNPLQDEWVLVSAHRMKRPWQGQVEPEPLKTVPRHDP
Retrocopy MSRGGTDSEQRQQASEADATKTAFLASEHQHIRYNPLQDEWVLVSAHRMKRPWQGQVEPEPLKTVPRHDP

Parental  LNPLCPGATRANGEVNPNYDGTFLFDNDFPALQPDAPNPGPSDHPLFQAQAARGVCKVMCFHPWSDVTLP
          LNPLCPGATRANGEVNPNYDGTFLFDNDFPALQPDAPNPGPSDHPLFQ.QAARGVCKVMCFHPWSDVTLP
Retrocopy LNPLCPGATRANGEVNPNYDGTFLFDNDFPALQPDAPNPGPSDHPLFQVQAARGVCKVMCFHPWSDVTLP

Parental  L-MSVPEIRAVVDAWASVTEDLGTQYPWVQIFENKGAMMGCSNPHPHCQVWASSFLPDIAQREERSQRAY
          L.MSVPEIRAVVDAWASVTEDLG.QYPWVQIFENKGAMMGCSNPHPHCQVWASSFLPDIAQREERSQRAY
Retrocopy L>MSVPEIRAVVDAWASVTEDLGAQYPWVQIFENKGAMMGCSNPHPHCQVWASSFLPDIAQREERSQRAY

Parental  HSQHGEPLLMEYGRQELLRKDRLVLTSEHWLVLVPFWAVWPFQTLLLPRRHVRRLPELTPTERDDLASIM
          HSQHGEPLLMEYGRQELLRKD.LVLTSEHWLVLVPFWAVW..QTLLLPRRHV..LPELTPTERDDLASIM
Retrocopy HSQHGEPLLMEYGRQELLRKDHLVLTSEHWLVLVPFWAVWTLQTLLLPRRHVWWLPELTPTERDDLASIM

Parental  KKLLTKYDNLFETSFPYSMGWHGAPTGSEAGAAWDHWQLHAHYYPPLLRSATVRKFMVGYEMLAQAQRDL
          KKLLTKYDNLFETS.PYSMGWHGAPTGSEAGA.WDHWQLHAHYYPPLLRSAT.RKFMVGYEML.QAQRDL
Retrocopy KKLLTKYDNLFETSLPYSMGWHGAPTGSEAGATWDHWQLHAHYYPPLLRSATHRKFMVGYEMLTQAQRDL

Parental  TPEQAAERLRALPEVHYRLRQKDKETAAV
          TPEQA.ERLRALPEVHYRLRQKDKETAA.
Retrocopy TPEQATERLRALPEVHYRLRQKDKETAAI

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	0.00 RPM	17.99 RPM
SRP017611_kidney	0.10 RPM	23.41 RPM
SRP017611_liver	0.00 RPM	15.65 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1903 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1903 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000024714	1 retrocopy	retro_ocun_1903 ,