RetrogeneDB ID: retro_ocun_1616

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018717:3830271..3830799(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021310
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STX3
• Ensembl ID: ENSOCUG00000013382
• Aliases: None
• Description: syntaxin 3 [Source:HGNC Symbol;Acc:11438]

Sequence

>retro_ocun_1616
CGGCTGGAGCAGCTGAAGGCCAAGCAGCTGACACAGGATGATGACACTGATGAGGTCGAGATCGCTATTGACAACACAGC
TTTCATGGATGAGGTCTTCTCAGAGATTGAAGAAACTCGGCTCAACATTGACAAGATCTCAGAGCACGTGGAGGAGGCCA
AGAAACTCTACAGTATCATTTTTTCTGCACCAATTCCAGAGCCAAAAACCAAGGATGACCTAGAGCAGCTCACAACTGAG
ATCAAGAAAAGAGCCAACAACGTCCGGAACAAGCTGAAGAGCATGGAGAGGCACATTGAAGAAGATGAGGTCTGGTCATC
TGCAGACCTTCGAATTAGGAAATCTCAGCACTCTGACCTCTCCCGGAAGTTTGTGGAGGTGATGACCAAATACAACGAAG
CTCAGGTGGACTTCCGGGAACGCAGCAAAGGGAGAATCCAGCGGCAGCTTGAAATCACTGGCAAAAAGACAACAGATGAG
GAACTGGAGGAGATATTAGAGAGTGGCAACCCAGCCATCTTACTTTCC

Alignment

ORF - retro_ocun_1616 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 61.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLIKLPVKQLTQDDDTDEVEIAIDNTAFMDEFFSEIEETRLNIDKISEHVEEAKKLYSIILSAPIPEPRK
          RL..L..KQLTQDDDTDEVEIAIDNTAFMDE.FSEIEETRLNIDKISEHVEEAKKLYSII.SAPIPEP.K
Retrocopy RLEQLKAKQLTQDDDTDEVEIAIDNTAFMDEVFSEIEETRLNIDKISEHVEEAKKLYSIIFSAPIPEP-K

Parental  MVSKSVLLVVTIKEQFGKTFLSFPGMERHIEEDEVRSSADLRIRKSQHSVLSRKFVEGMTKYNEAQVDFR
          .......L...IK............MERHIEEDEV.SSADLRIRKSQHS.LSRKFVE.MTKYNEAQVDFR
Retrocopy TKDDLEQLTTEIKKRANNVRNKLKSMERHIEEDEVWSSADLRIRKSQHSDLSRKFVEVMTKYNEAQVDFR

Parental  ERSKGRIQRQLEITGKKTTDEELEEMLESGNPAIFTS
          ERSKGRIQRQLEITGKKTTDEELEE.LESGNPAI..S
Retrocopy ERSKGRIQRQLEITGKKTTDEELEEILESGNPAILLS

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	1.71 RPM	14.51 RPM
SRP017611_kidney	2.94 RPM	18.14 RPM
SRP017611_liver	0.31 RPM	2.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1616 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1616 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000026681	1 retrocopy	retro_mluc_105,
Oryctolagus cuniculus	ENSOCUG00000013382	1 retrocopy	retro_ocun_1616 ,