RetrogeneDB ID: retro_ocun_961

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:3204413..3205548(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025083
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: METTL25
• Ensembl ID: ENSOCUG00000017825
• Aliases: None
• Description: methyltransferase like 25 [Source:HGNC Symbol;Acc:26228]

Sequence

>retro_ocun_961
ATGGCGGCTGCAGGTCTTCTCCCGGTGACCCAGGACCTGCCCACTCTGCATGCTAAGTTGCAGGGGCTGCTATGGTTCCT
CAGGGACGCTTTATCCATTTCGAATGCCCATACGGTGGACTTTTACACAGAGTCCCTGTGGGAAGAGCTGGTCGACTTGC
CCCCGGAGACGGTGCTCGCAGCGCTGAGGAAGTGGCACTGGAGGCGCAGGCCCGGCTTGCGGAGTCGCGCCCCCTGCTGG
AAGCAGAGATGGGGTCAGGTATTACTGATTTTCCCAAAATATTTAGTGAAACTTCTCAGAAGCTGGTGAGTGCAGAAGCC
TTTGCTCTGGCTGCAAAATGTTTTTCCATGCAGAACTTGGGAATATGTACTCCTTTTGAACAGTTGCTTGTAGCCCTTCA
AGGAAATCAAAAGCAGAAAACTGGTGAAAATGTGAAGCCAGTTGAGTTTATGAATGTGAAAAAATCTCATGAAGTTCAGG
CAATGTCAGAGCTGATCAGCAGTATTGCTGATTACTGTGGAATCAAACAGATAATTGACTTGGGTTCTGGTAAAGGCTAC
CTAAGCTCCTTTTTGTCCTTGAAATATGGCTTAAAAGTGTATGGAATTGATTCCTCAAATACTAATACTCATGGAGCTGA
AGAGAGAAACAGGAAATTGAAGAAACACTGGAAACTCTATCATACTCAGTCAAGATTGGATGTCAGTGGACTGACATTAA
AAATGGCAACAGAGACCAAAGAACGAAATGAAATGAAATATAAAGCAGATATTGCAGAAATTTGTAACAACAGACCGGCA
AATCAAGAAAAAATATCAGCCTCAAATTTTTTGCCAGCTGTTTCAGAATCTGTAATTTCTCACATCAGAAAAAAAAATGG
AAAACCTACATACTCAGTCACATCTAGAAGAAAATTTTTGTTTTGATAATGCGTTGTCCCTTATAGACCTTTTGCCTGTT
AATTCCTCGGAGCCTACTTCTTCATCACAAATACCTAGCAAAGAAATAGAAATGCTTGAAGAAAATAAAGAGAAGAAAAA
TGACATCAAGGTCACATGAATCAAATATATATTCGCCTTTAACCTCTTTTATCACTGCTGATTCAGAACTACATGATATT
ATTAAAGATCTGGAG

Alignment

ORF - retro_ocun_961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.55 %
• Parental protein coverage: 62.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAAGLLPVTQDLPTLHAKLQGLLWFLRDALSISNAHTVDFYTESLWEELVDLPPETVLAALRK-SALEP
          MAAAGLLPVTQDLPTLHAKLQGLLWFLRDALSISNAHTVDFYTESLWEELVDLPPETVLAALRK..ALE.
Retrocopy MAAAGLLPVTQDLPTLHAKLQGLLWFLRDALSISNAHTVDFYTESLWEELVDLPPETVLAALRK<VALEA

Parental  QARLAESRPLLEAEMGSGITDFPKIFSETSQKLVSAEAFALAAKCFSMQNLGICTPFEQLLVALQGNQKQ
          QARLAESRPLLEAEMGSGITDFPKIFSETSQKLVSAEAFALAAKCFSMQNLGICTPFEQLLVALQGNQKQ
Retrocopy QARLAESRPLLEAEMGSGITDFPKIFSETSQKLVSAEAFALAAKCFSMQNLGICTPFEQLLVALQGNQKQ

Parental  KTGENVKPVEFMNVKKSHEVQAMSELISSIADYCGIKQIIDLGSGKGYLSSFLSLKYGLKVYGIDSSNTN
          KTGENVKPVEFMNVKKSHEVQAMSELISSIADYCGIKQIIDLGSGKGYLSSFLSLKYGLKVYGIDSSNTN
Retrocopy KTGENVKPVEFMNVKKSHEVQAMSELISSIADYCGIKQIIDLGSGKGYLSSFLSLKYGLKVYGIDSSNTN

Parental  THGAEERNRKLKKHCKLYHTQSRLDVSGLTLKMATETKERNEMKYKAGIAEICNNRPANQEKISASNFLP
          THGAEERNRKLKKH.KLYHTQSRLDVSGLTLKMATETKERNEMKYKA.IAEICNNRPANQEKISASNFLP
Retrocopy THGAEERNRKLKKHWKLYHTQSRLDVSGLTLKMATETKERNEMKYKADIAEICNNRPANQEKISASNFLP

Parental  AVSESVISHIRKK-MENLRTQSHLEENFCFDNALSLIDLLPVNSSEPTSSSQIPS-KEIEMLEENKERRK
          AVSESVISHIRKK.MENL.TQSHLEENFCFDNALSLIDLLPVNSSEPTSSSQIPS.K....L...K.RRK
Retrocopy AVSESVISHIRKK>MENLHTQSHLEENFCFDNALSLIDLLPVNSSEPTSSSQIPS>KK*KCLKKIK-RRK

Parental  MTSKSHESNIYSPLTSFITADSELHDIIKDLE
          MTS.SHESNIYSPLTSFITADSELHDIIKDLE
Retrocopy MTSRSHESNIYSPLTSFITADSELHDIIKDLE

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	3.20 RPM
SRP017611_kidney	0.00 RPM	4.87 RPM
SRP017611_liver	0.00 RPM	2.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_961 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_961 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	ENSOCUG00000017825	1 retrocopy	retro_ocun_961 ,