RetrogeneDB ID: retro_ocun_1458

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:88666911..88667722(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMS
• Ensembl ID: ENSOCUG00000006016
• Aliases: None
• Description: spermine synthase [Source:HGNC Symbol;Acc:11123]

Sequence

>retro_ocun_1458
AAGGAGAGATCAACAGCCTTGAACAAAGTAGAAGAAACAATGAAAGAATTGAGTCAGGGCGGTACTGGGAGGGTGAAGCG
ATTGCCGCCCATTGTTTGAGGAGCCATTGACAGATAGTGGCCCACTGCTGCCGGGCGCCTGGTTGAGGATGACATAGGTG
ACATGGTGTATGATGAAGGCTCGCCTTATCAGAACATTAAAATTGTACACTCAAATCAATTCGGAAATATTCCAATCTTC
AGTGGGGATGTCAACTTGGTGGAGAATAATTTGGTGTATACCTGGGCCAGCATGTGCAGTGGAAAAGATTAATACACAAT
GATCCTGGGAGGTGGAGATGGAGGCATATTATGTGAAATAGTCAGACTGAAACCAAAGGTGGTCACTATGGTGGAAAGTG
ACCAAAGGTGATTGATGGATGTGAGAAATGCAGGAGAAAACTGTGTGACAACGTCTTAGACGATCCTAGCGGAGACTGCC
ATCGGTTCTAATAGAAGACTGCATTCCAGTACTGAAGAGGTACGCCAAAGAAGGGAGAGGGTTTGCCTATTTGATTAATG
ATTTAACAACTGTTCCAATCCCTACATCTTCAGAGGAAGATTCCACATGGGAGTTTCTCAGACTGATTCTTGATCTCTCT
ATGAAAGTACTGAAATAGGATGTGAAGTACTTTACTACAAGGGAACTGTGTCAGTGTGATGGAAGCTCTGTCACTCTACG
AAGTACAGCCCGGGAATTGTCCTGTGGAATTATCAAAGGATACGGCCTGTGTGCCTCATACTTGGTATGAGGTGGGTATT
TTACATTGTTT

Alignment

ORF - retro_ocun_1458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.28 %
• Parental protein coverage: 78.31 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EEIDSLLNKVEERMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKIL
          .E....LNKVEE.MKELSQ..TGRVKRLPPIV.G.AIDR.WPTA.GRLVE.DI...VYDE.SPYQNIKI.
Retrocopy KERSTALNKVEETMKELSQGGTGRVKRLPPIV*G-AIDR*WPTAAGRLVEDDIGDMVYDEGSPYQNIKIV

Parental  HSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQ
          HS.QFGNI.I.SGDVNL.E..L.YT.A.M.SGK..YT.....ILGGGDGGILCEIV.LKPK.VTMVE.DQ
Retrocopy HSNQFGNIPIFSGDVNLVENNLVYTWASMCSGKD*YT----MILGGGDGGILCEIVRLKPKVVTMVESDQ

Parental  M-VIDGCKKYMRKTCGDVLDNLNGDCYQ-VLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDST
          ..VIDGC.K..RK.C..VLD...GDC...VLIEDCIPVLKRYAKEGR.F.Y.INDLT.VPI.TS.EEDST
Retrocopy R<VIDGCEKCRRKLCDNVLDDPSGDCHR<VLIEDCIPVLKRYAKEGRGFAYLINDLTTVPIPTSSEEDST

Parental  WEFLRLILDLSMKVLKQDGKYFT-QGNCVNLTEALSLYEEQLGRLYCPVEFSKETVCVP-SYLELWVFYT
          WEFLRLILDLSMKVLK.D.KYFT.QGNCV...EALSLYE.Q.G...CPVE.SK.T.CVP.SYL......T
Retrocopy WEFLRLILDLSMKVLK*DVKYFT>QGNCVSVMEALSLYEVQPGN--CPVELSKDTACVP<SYLV*GGYFT

Parental  VW
          ..
Retrocopy LF

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	81.90 RPM
SRP017611_kidney	0.00 RPM	74.50 RPM
SRP017611_liver	0.00 RPM	69.06 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1458 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1458 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018382	1 retrocopy	retro_btau_1412,
Canis familiaris	ENSCAFG00000013284	3 retrocopies	retro_cfam_1076, retro_cfam_1995, retro_cfam_613,
Callithrix jacchus	ENSCJAG00000033933	1 retrocopy	retro_cjac_518,
Cavia porcellus	ENSCPOG00000006176	2 retrocopies	retro_cpor_729, retro_cpor_889,
Echinops telfairi	ENSETEG00000010098	2 retrocopies	retro_etel_1066, retro_etel_1540,
Gorilla gorilla	ENSGGOG00000003123	3 retrocopies	retro_ggor_1335, retro_ggor_2437, retro_ggor_3009,
Microcebus murinus	ENSMICG00000000192	3 retrocopies	retro_mmur_1421, retro_mmur_1484, retro_mmur_699,
Myotis lucifugus	ENSMLUG00000013185	3 retrocopies	retro_mluc_471, retro_mluc_530, retro_mluc_92,
Monodelphis domestica	ENSMODG00000007897	1 retrocopy	retro_mdom_412,
Nomascus leucogenys	ENSNLEG00000009955	4 retrocopies	retro_nleu_1664, retro_nleu_2200, retro_nleu_2208, retro_nleu_2755,
Oryctolagus cuniculus	ENSOCUG00000006016	2 retrocopies	retro_ocun_1458 , retro_ocun_1918,
Pongo abelii	ENSPPYG00000020182	4 retrocopies	retro_pabe_2649, retro_pabe_2810, retro_pabe_3752, retro_pabe_38,
Pteropus vampyrus	ENSPVAG00000016785	1 retrocopy	retro_pvam_524,
Rattus norvegicus	ENSRNOG00000007688	2 retrocopies	retro_rnor_1934, retro_rnor_938,
Tupaia belangeri	ENSTBEG00000012109	3 retrocopies	retro_tbel_1630, retro_tbel_1893, retro_tbel_3570,
Vicugna pacos	ENSVPAG00000007543	1 retrocopy	retro_vpac_50,