RetrogeneDB ID: retro_ocun_1540

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02081496:2273..3404(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000000602
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ERGIC2
• Ensembl ID: ENSOCUG00000017255
• Aliases: None
• Description: ERGIC and golgi 2 [Source:HGNC Symbol;Acc:30208]

Sequence

>retro_ocun_1540
ATGAGGCGACTGAATCGGAAAAAAACCTTAAGTTTGGTCAAAGAGTTGGACGCCTTTCCCAAGGTTCCTGACAGCTATGT
AGAGACTTCGGCCAGCGGGGGTACAGTTTCTCTGATAGCGTTTACCACTATGGCTTTATTAACAATAATGGAATTCTCAG
TGTATCAAGATACATGGATGAAGTATGAATATGAAGTAGACAAGGACTTTTCTAGCAAATTGAGAATTAATATAGATATT
ACTGTGGCCATGAAGTGTCAGTATGTTGGAGCAGATGTGTTAGATTTAGCAGAAACAATGGTTGCATCTGCAGATGGTCT
AGTTTATGAACCAGCAATATTTGATCTTTCACCACATCAAAGAGAGTGGCAGAGGATGCTGCAGCTGATTCAGAGTAGGC
TGCAAGAAGAGCATTCACTTCAAGATGTCATATTTAAAAGTGCTTTTAAAAGCCCTTCAACAGCACTTCCACCAAGGGAG
GATGACTCGCTGCAGTCTCCAGATGCGTGCAGGATTCACGGGCACCTCTATGTCAACAAAGTAGCAGGGAACTTCCACAT
AACCGTGGGCAAGGCAATTCCACATCCCCGAGGCCATGCACACTTGGCAGCTCTTGTCAACCATGACTCTTACAATTTCT
CTCACAGAATAGATCATTTGTCTTTTGGAGAACTTGTTCCGGGAATCATCAATCCTTTAGATGGAACTGAAAAAATTGCT
ATAGATCACAACCAGATGTTCCAGTATTTTATTACAATTGTGCCAACAAAGCTACATACTTACAAGATTTCAGCAGATAC
CCATCAGTTTTCTGTGACAGAAAGGGAACGCATCATCAACCACGCTGCGGGCAGCCACGGCGTCTCGGGGATATTCATGA
AGTACGACCTCAGCTCTCTGATGGTGACAGTGACTGAGGAGCACATGCCGTTCTGGCAGTTTTTTGTGCGGCTTTGTGGC
ATAGTTGGAGGGATCTTTTCAACAACAGGAATGTTACATGGAATTGGGAAATTTATAGTTGAAATAATTTGCTGTCGTTT
CCGACTTGGATCCTCTAAGCCCGTCACTTCTGTCCCTTTTGAGGATGGCCACACAGACAACCACTTACCTCTTCTAGAAA
ACAATGCGCAT

Alignment

ORF - retro_ocun_1540 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRLNRKKTLSLVKELDAFPKVPDSYVETSASGGTVSLIAFTTMALLTIMEFSVYQDTWMKYEYEVDKDF
          MRRLNRKKTLSLVKELDAFPKVPDSYVETSASGGTVSLIAFTTMALLTIMEFSVYQDTWMKYEYEVDKDF
Retrocopy MRRLNRKKTLSLVKELDAFPKVPDSYVETSASGGTVSLIAFTTMALLTIMEFSVYQDTWMKYEYEVDKDF

Parental  SSKLRINIDITVAMKCQYVGADVLDLAETMVASADGLVYEPAIFDLSPHQREWQRMLQLIQSRLQEEHSL
          SSKLRINIDITVAMKCQYVGADVLDLAETMVASADGLVYEPAIFDLSPHQREWQRMLQLIQSRLQEEHSL
Retrocopy SSKLRINIDITVAMKCQYVGADVLDLAETMVASADGLVYEPAIFDLSPHQREWQRMLQLIQSRLQEEHSL

Parental  QDVIFKSAFKSPSTALPPREDDSLQSPDACRIHGHLYVNKVAGNFHITVGKAIPHPRGHAHLAALVNHDS
          QDVIFKSAFKSPSTALPPREDDSLQSPDACRIHGHLYVNKVAGNFHITVGKAIPHPRGHAHLAALVNHDS
Retrocopy QDVIFKSAFKSPSTALPPREDDSLQSPDACRIHGHLYVNKVAGNFHITVGKAIPHPRGHAHLAALVNHDS

Parental  YNFSHRIDHLSFGELVPGIINPLDGTEKIAIDHNQMFQYFITIVPTKLHTYKISADTHQFSVTERERIIN
          YNFSHRIDHLSFGELVPGIINPLDGTEKIAIDHNQMFQYFITIVPTKLHTYKISADTHQFSVTERERIIN
Retrocopy YNFSHRIDHLSFGELVPGIINPLDGTEKIAIDHNQMFQYFITIVPTKLHTYKISADTHQFSVTERERIIN

Parental  HAAGSHGVSGIFMKYDLSSLMVTVTEEHMPFWQFFVRLCGIVGGIFSTTGMLHGIGKFIVEIICCRFRLG
          HAAGSHGVSGIFMKYDLSSLMVTVTEEHMPFWQFFVRLCGIVGGIFSTTGMLHGIGKFIVEIICCRFRLG
Retrocopy HAAGSHGVSGIFMKYDLSSLMVTVTEEHMPFWQFFVRLCGIVGGIFSTTGMLHGIGKFIVEIICCRFRLG

Parental  SSKPVTSVPFEDGHTDNHLPLLENNAH
          SSKPVTSVPFEDGHTDNHLPLLENNAH
Retrocopy SSKPVTSVPFEDGHTDNHLPLLENNAH

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	1.21 RPM	15.12 RPM
SRP017611_kidney	1.62 RPM	18.14 RPM
SRP017611_liver	0.54 RPM	8.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1540 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1540 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015668	1 retrocopy	retro_cpor_824,
Ornithorhynchus anatinus	ENSOANG00000010582	1 retrocopy	retro_oana_32,
Oryctolagus cuniculus	ENSOCUG00000017255	1 retrocopy	retro_ocun_1540 ,
Pongo abelii	ENSPPYG00000004390	1 retrocopy	retro_pabe_657,
Rattus norvegicus	ENSRNOG00000001852	1 retrocopy	retro_rnor_1557,
Sarcophilus harrisii	ENSSHAG00000004822	1 retrocopy	retro_shar_386,
Tupaia belangeri	ENSTBEG00000011223	1 retrocopy	retro_tbel_3783,