RetrogeneDB ID: retro_ocun_1355

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:38821009..38821860(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024285
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTAP
• Ensembl ID: ENSOCUG00000012289
• Aliases: None
• Description: methylthioadenosine phosphorylase [Source:HGNC Symbol;Acc:7413]

Sequence

>retro_ocun_1355
ATGGCCTCAGGTGCCGCCACCACTGCCACCGTGAAGACTGGAATAATTGGTGGAAGAGGCCTGGATGATCCAGAAATTTT
AGAAGGAAGAACTGAAAAATATGTGGATACTCCATTTGGCAAGCCATCCAATGCCTTAATTTTGGGGAAAATAAAAAATG
TTGATTGCGCCCTCCTTGCCATGCATGGGAGGCAGCACACCATCATGCCTTCCAAAGTCAACTACCAGGCAAACATCTGG
GCTTTGAAGGAGGAGGGTTATACACATGTCATAGTGACCACAGCTTGTGGCTCCTCGAGGGAGGAGATTCAGCCCGGCGA
TATTGTCATTAACAATCAGTTCATTGACAGGACCATGACAAGGCCTCAGACCTTCTATGATGGAAGTCATTCCTGTGTCA
GAGGAGTGTGCCACATTCCAATGGCTGAGCCGTTTTGCCCCAGAACAAGAGAGGTCCTCATAGAGACTGCTAAGAAGCTA
GGACTCCGGTGCCACTCAAAGGGGTCAATGGTCACAACTGAAAGACCTCGATTTAGCTCCTGGGCAGCAAGCTTCATGTT
CCGCACCTGGGGAGCGGATGTCATCAATATGACCACTGTTCCAGAGGTGGTTCTTGCCAAAGAGGCTGGAATTTGCCTTG
CAAGTATTGCCGTGGCAACGGATTATGATTGTGGAAGAAGCACGAGGAAGCAGTTTCAGTGGGCCGGGTCTTAAAGACCC
TGAAAGAAAATGCCAATAAAGCCAAAGGTTTGCTCCTCACCACCATACCTCAGATAGGGTTCACAGAGTGGTCTGAAACC
CTCCATAACCTGAAGAATATGGCCCAGTTTTCTGTTTTATTACCAAGACAT

Alignment

ORF - retro_ocun_1355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGAATTAAVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIKNVDCVLLARHGRQHTIMP
          MASGAATTA.VK.GIIGG.GLDDPEILEGRTEKYVDTPFGKPS.ALILGKIKNVDC.LLA.HGRQHTIMP
Retrocopy MASGAATTATVKTGIIGGRGLDDPEILEGRTEKYVDTPFGKPSNALILGKIKNVDCALLAMHGRQHTIMP

Parental  SKVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIVIIDQFIDRTMTRPQTFYDGSHSCARGVCHIP
          SKVNYQANIWALKEEG.THVIVTTACGS.REEIQPGDIVI..QFIDRTMTRPQTFYDGSHSC.RGVCHIP
Retrocopy SKVNYQANIWALKEEGYTHVIVTTACGSSREEIQPGDIVINNQFIDRTMTRPQTFYDGSHSCVRGVCHIP

Parental  MAEPFCPKTREVLIETAKKLGLRCHSKGTMVTIEGPRFSSRAESFMFRTWGADVINMTTVPEVVLAKEAG
          MAEPFCP.TREVLIETAKKLGLRCHSKG.MVT.E.PRFSS.A.SFMFRTWGADVINMTTVPEVVLAKEAG
Retrocopy MAEPFCPRTREVLIETAKKLGLRCHSKGSMVTTERPRFSSWAASFMFRTWGADVINMTTVPEVVLAKEAG

Parental  ICYASIAMATDYDC-WKEHEEAVSVDRVLKTLKENANKAKSLLLTTIPQIGSTEWSETLHNLKNMAQFSV
          IC.ASIA.ATDYDC.WK.HEEAVSV.RVLKTLKENANKAK.LLLTTIPQIG.TEWSETLHNLKNMAQFSV
Retrocopy ICLASIAVATDYDC<WKKHEEAVSVGRVLKTLKENANKAKGLLLTTIPQIGFTEWSETLHNLKNMAQFSV

Parental  LLPRH
          LLPRH
Retrocopy LLPRH

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	9.88 RPM
SRP017611_kidney	0.10 RPM	33.04 RPM
SRP017611_liver	0.15 RPM	14.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1355 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1355 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1355 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355 , retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792,