RetrogeneDB ID: retro_ocun_1207

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:111879601..111880482(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AEBP2
• Ensembl ID: ENSOCUG00000016677
• Aliases: None
• Description: AE binding protein 2 [Source:HGNC Symbol;Acc:24051]

Sequence

>retro_ocun_1207
AGCATAAGCAGTCTATAATGGATGTAGACAGCACAATTTCCAGTGGGCGTTCAACTCCAGCAATAATGAATGGACAAGGA
AGCACTACTTCTTCAAGCAAAAATATTGCCTATAATTGTTGTTGGGACCAGTGCCAGGCTTGCTTCAACTCTAGCCCAGA
TCTGGCAGATCACATCCATTCCATACATGTAGGTGATCAGCGAGGAGGGGTATTTGTTTGCTTATGGAAAGATTGCAAAG
TATATAACACTCCATCAACAGTCAAAGTTGGCTACAGAGGCACATGCTGACGCACAGTGGAGACAAACCTTTCAAGTATG
TTGTTGGCGGCTGCAATGCCAGCTTTGCTTCTCAGGGAGGGCTAGCTCGCCATGTACCCACACACCTCAGTCAGCAGAAC
TCCTCCAAAGTTTCTAGCCAGCCAAAGGCCAAAGAAGAATCTCCTTCTAAAGCTGGAATGAACAAAAGGAGGAAATTAAA
GAGCAAAAGACGACGTTCATTACCGTGACCACATGATTTCTTCGATGCACAAACACTGGATGTGATAAGACATCGAGCCA
TTTGCTTTAACCTCTCAGCTCATATAGAAAGTTTAGGGAAAGGCCACAGTGTTGTTTTTCATAGTACTTTAATAGCTAAG
AGAAAAGAGGATTCTGGAAAGATAAAGCTTTTGCTTCATTGGATGCCTGAAGACATTCTGCTAGATGTCTGGGTGAATGA
AAGTGAACGACATCAGTTAAAAACTAAAGTAGTTCATTTATCAAAGCTACCCAAAGATACTGCCTTGCTTTTGGACCCAA
ACATATACAGAACAATGCCACAGAAGAGGGTTGAAGAGAACTCTGATAAGAAAAGTGTTCAATTTGTATTTAAGCAAACA
G

Alignment

ORF - retro_ocun_1207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SISS-TIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHIRSIHVDGQRG
          SISS..IMDVDSTISSGRSTPA.MNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHI.SIHV..QRG
Retrocopy SISS<SIMDVDSTISSGRSTPAIMNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHIHSIHVGDQRG

Parental  GVFVCLWKGCKVYNTPST-SQSWLQRHMLTHSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQQNSSKV
          GVFVCLWK.CKVYNTPST.SQSWLQRHMLTHSGDKPFK.VVGGCNASFASQGGLARHVPTH.SQQNSSKV
Retrocopy GVFVCLWKDCKVYNTPST<SQSWLQRHMLTHSGDKPFKYVVGGCNASFASQGGLARHVPTHLSQQNSSKV

Parental  SSQPKAKEESPSKAGMNKRRKLKNKRRRSLPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFH
          SSQPKAKEESPSKAGMNKRRKLK.KRRRSLP.PHDFFDAQTLD.IRHRAICFNLSAHIESLGKGHSVVFH
Retrocopy SSQPKAKEESPSKAGMNKRRKLKSKRRRSLP*PHDFFDAQTLDVIRHRAICFNLSAHIESLGKGHSVVFH

Parental  STVIAKRKEDSGKIKLLLHWMPEDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKR-
          ST.IAKRKEDSGKIKLLLHWMPEDIL.DVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKR.
Retrocopy STLIAKRKEDSGKIKLLLHWMPEDILLDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKR>

Parental  LKRTLIRKVFNLYLSKQ
          LKRTLIRKVFNLYLSKQ
Retrocopy LKRTLIRKVFNLYLSKQ

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	0.06 RPM	14.51 RPM
SRP017611_kidney	0.00 RPM	8.92 RPM
SRP017611_liver	0.00 RPM	4.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1207 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007440	1 retrocopy	retro_cpor_431,
Myotis lucifugus	ENSMLUG00000006293	1 retrocopy	retro_mluc_1637,
Oryctolagus cuniculus	ENSOCUG00000016677	2 retrocopies	retro_ocun_1207 , retro_ocun_1672,
Rattus norvegicus	ENSRNOG00000008929	1 retrocopy	retro_rnor_875,