RetrogeneDB ID: retro_ocun_1092

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:43135255..43136402(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024237
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSAT1
• Ensembl ID: ENSOCUG00000007765
• Aliases: None
• Description: phosphoserine aminotransferase 1 (PSAT1), mRNA [Source:RefSeq mRNA;Acc:NM_001082271]

Sequence

>retro_ocun_1092
GGGAGGGGGAAGGCAGCCAGCGCTGGGCGCACACTTGGCGCGGCGCGGCCGGGGACACCCGCTGGACACACTGTGGCTCC
TCAGTAGCTGACTCACCGCCCGCACCGCGGCGCCATGGATTCTCTGAGGCCGATTGTCAACTTCAGGTCGGGCCCGCCAA
GCTTCGTGCCCGGTATTGTTAGAGATACAGGAAGAATTACTGGACTACAAAAGACTTGGCATTAGTGCCCTTGAAATGAG
TCATAGGTTCTCAGATTTTGCCAAGATTGTTCACAACACAGAGAATCATGTGGGGGAATTGTTAGCAGTTCCAGACAAAT
ACAAGGTGATTTTTCTGCAAGGAGGTGGCCTTGGCCAGTTCAGTGCTGTCCCCTTAAACCTGACTGGCCTGAAACCCGGA
AGGTGTGCTGACTATGTGGTGACAGGGCTTTGGCCAGCAAAGGCTGCAGAAGAAGCTAAGAAGTTTGGGACTGTGACTAT
CATCCACCCTAAACTGTGGAGTTACACAAAAATCCCAGGTCCAAGCATCTGGAACCTTAATCCAGATGCCTCCTACGTGT
ACTATTGCACAAATGAGACAGTGCACGGCGTGGAGTTTGACTTCGTGCCTGATGTCAAGGGAGCCATTCTGGTTTGTGAC
ATGACCACAAACTTCCTCTCCAGGCCAGCAGATGTTTCCAAGTTTGGTGTGATTTTTGCTGGTGCCCAAAAGAACGTGGG
CTCTGCAGGAGCCACGGTGGTGATTGTCCGCGATGACCTGCTGGGGTTCGCCCTCCGAGACTGCCCCTCTGTCCTGGAGT
ACACAGTGCAGGCCACAAGCAACTCCTTGTACAACACGCCCCGTGTTTTAGCCTCTGTGTCGTGAGCTTGGTCCTGGAGC
AGATTAAGAACAGTGGTGGGGCAGCTGCCACAAAGAAACTCAGCACCATCAAGTCTCAAAAGATTTATGAAATTATCAAT
AACTAGCAAGGATTCTACCTCTGCCTGGTGGAGCCCCGAAATGGAAGCATGATGAATATTCCATCCCATATCGGCAACAC
CAGGGGGGACGAAGCTTTAGAAAAAATGATTCCTCAATAAAGCTCTGGAGCTCCATATGATCTCCCTGAAAGCACCCAGG
TCCATAGGAGGCATCTGGGTCTCTCTA

Alignment

ORF - retro_ocun_1092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.12 %
• Parental protein coverage: 79.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GRRKAASAGRTLGAARPR-GTHWTRRGSSVADSPPAPQRHAMDSPRQIVNFGPGPAKLPHSVLLEIQKEL
          GR.KAASAGRTLGAARP...T.WT..GSSVADSPPAP.RH...........G..PAKL.........K..
Retrocopy GRGKAASAGRTLGAARPG<DTRWTHCGSSVADSPPAPRRHGFSEADCQLQVG--PAKLRARYC*RYRKNY

Parental  LDYKGLGI-SVLEMSHRSSDFAKIVNNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKPGRC
          ...K.L...S.LEMSHR.SDFAKIV.NTEN.V.ELLAVPD.YKVIFLQGGG.GQFSAVPLNL.GLKPGRC
Retrocopy WTTKDLAL<SALEMSHRFSDFAKIVHNTENHVGELLAVPDKYKVIFLQGGGLGQFSAVPLNLTGLKPGRC

Parental  ADYVVTGAWSAKAAEEAKKFGTVNIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFVPDV
          ADYVVTG.W.AKAAEEAKKFGTV.I.HPKL.SYTKIP.PS.WNLNPDASYVYYC.NETVHGVEFDFVPDV
Retrocopy ADYVVTGLWPAKAAEEAKKFGTVTIIHPKLWSYTKIPGPSIWNLNPDASYVYYCTNETVHGVEFDFVPDV

Parental  KGAILVCDMSSNFLSRPVDVSKFGVIFAGAQKNVGAAGVTVVIVRDDLLGFALRECPSVLEYKVQATSSS
          KGAILVCDM..NFLSRP.DVSKFGVIFAGAQKNVG.AG.TVVIVRDDLLGFALR.CPSVLEY.VQATS.S
Retrocopy KGAILVCDMTTNFLSRPADVSKFGVIFAGAQKNVGSAGATVVIVRDDLLGFALRDCPSVLEYTVQATSNS

Parental  LYNTP-PCFSIYVMGLVLEWIKNNGGAAAMKKLSTIKSQMIYEIIDNSQGFYVCPVEPRNRSMMNIPFRI
          LYNTP.PCFS..V..LVLE.IKN.GGAAA.KKLSTIKSQ.IYEII.N.QGFY.C.VEPRN.SMMNIP..I
Retrocopy LYNTP<PCFSLCVVSLVLEQIKNSGGAAATKKLSTIKSQKIYEIINN*QGFYLCLVEPRNGSMMNIPSHI

Parental  GNAKGDEALEKR-FLDKALELHMISLKGHRSVGGVRVSL
          GN..GDEALEK..FL.KALELHMISLK..RS.GG..VSL
Retrocopy GNTRGDEALEKM>FLNKALELHMISLKAPRSIGGIWVSL

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	133.34 RPM
SRP017611_kidney	0.00 RPM	309.34 RPM
SRP017611_liver	0.08 RPM	120.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1092 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1092 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1092 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006898	1 retrocopy	retro_amel_375,
Bos taurus	ENSBTAG00000013960	1 retrocopy	retro_btau_1658,
Canis familiaris	ENSCAFG00000001570	1 retrocopy	retro_cfam_269,
Choloepus hoffmanni	ENSCHOG00000003817	1 retrocopy	retro_chof_2702,
Callithrix jacchus	ENSCJAG00000003319	1 retrocopy	retro_cjac_1203,
Echinops telfairi	ENSETEG00000004158	1 retrocopy	retro_etel_99,
Homo sapiens	ENSG00000135069	3 retrocopies	retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla	ENSGGOG00000015480	1 retrocopy	retro_ggor_407,
Loxodonta africana	ENSLAFG00000017917	2 retrocopies	retro_lafr_1249, retro_lafr_660,
Macaca mulatta	ENSMMUG00000011868	2 retrocopies	retro_mmul_1029, retro_mmul_2341,
Mustela putorius furo	ENSMPUG00000012566	1 retrocopy	retro_mputfur_808,
Nomascus leucogenys	ENSNLEG00000002989	3 retrocopies	retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus	ENSOCUG00000007765	1 retrocopy	retro_ocun_1092 ,
Pongo abelii	ENSPPYG00000019313	3 retrocopies	retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes	ENSPTRG00000021045	2 retrocopies	retro_ptro_1606, retro_ptro_316,
Rattus norvegicus	ENSRNOG00000013971	1 retrocopy	retro_rnor_1663,
Tupaia belangeri	ENSTBEG00000012946	1 retrocopy	retro_tbel_1577,
Tarsius syrichta	ENSTSYG00000000093	2 retrocopies	retro_tsyr_1073, retro_tsyr_1212,