RetrogeneDB ID: retro_xmac_16

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556664.1:4069853..4070969(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019501
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: npy2rl
• Ensembl ID: ENSXMAG00000008242
• Aliases: None
• Description: neuropeptide Y receptor Y2, like [Source:ZFIN;Acc:ZDB-GENE-111115-4]

Sequence

>retro_xmac_16
ATGAGCCCACTTGACACATCCAACGTCACAGCAGAAGTGGAGCCTAGCGAAAGTGATCTGTCGTTTTTGTTCAACGACAG
CTCTGATTCATACCAGCCCGGTTTCAGCTCTGATGTCACCAAGCACCTTGGAGTCCAAATCACTCTAATAATGGCTTATT
CCTTAATAATCCTGCTGGGGCTGCTGGGCAATTCCCTCGTCATCTACATGATTATTCGCTACAGAAACATGCGGACAGTG
ACCAACTACTTCATAGCCAACCTGGCTTTGGCAGACCTTCTGATGGTCACTCTGTGCCTGCCCTTTACTCTGATTTACAC
TCTGCTGGATGAATGGAAGTTTGGTGCCGTGTTGTGCCACATGGTCCCATTTGCCCAAGCTCTGAGTGTTCATGTGTCCA
TCCTGACCCTGACTGTCATAGCTCTGGAGCGTTACCGCTGCATTGTCTTCCACCTTGGTCGACGGCTCACCTGGCATTCC
AGCCTCTTCATCATGGCATTCACCTGGACTATTTCTTCTGTCCTGGCAGCTCCTCTTGCTATCTTCAGAGAATATCGCTA
TGAAGAGATTCCTCCTATCAATCTGCGCATGCCTGTCTGCTCTGAGAAGTGGCCCCATGGCATCAACAGGGATGGAGTCA
TCTACAGTCTCTCAATGATCCTACTATTGTACATTCTTCCTTTAGCAATCATTAGTTATGCATACATATGCATTTGGGTC
AAACTGAAAAACCATGTCAGTCCGTCCAGCCGTAACGACAGCATCAACCGACGCAAGAAAACCACAAAGATGCTAGCACT
GGTAGTAGTGGTGTTTGCAACCAGTTGGCTGCCTTTACATGTGCTCCAGCTGGCCACTGATCTGGACTTGGTGCTCCGAT
TTGAGGAGTATAAGCTCATCTTCACAGTGTTTCACATCGTGGCTATGTGCCCTACCTTCACCAACCCTCTCCTCTATGGA
TGGATGAATAAAAACTACAGGAATGGCTTCATAATGGTGTTCCGTTGCGAGGACAAGGCAGATACTTTCCACCCAGATGG
GTCATTCAGGACACGCTCTGTAAGAGGGCCCACTCTGAACGGTCGTAACAGCAGACACCCTACTACTGCTGTATGA

Alignment

ORF - retro_xmac_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.81 %
• Parental protein coverage: 76.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FPEDPIRLLSVQVVLILAYSTIIGLGVLGNSLVIYVIYRFKTLRTVTNFFIANLAVADLLVNTLCLPFTL
          F..D....L.VQ..LI.AYS.II.LG.LGNSLVIY.I.R....RTVTN.FIANLA.ADLL..TLCLPFTL
Retrocopy FSSDVTKHLGVQITLIMAYSLIILLGLLGNSLVIYMIIRYRNMRTVTNYFIANLALADLLMVTLCLPFTL

Parental  VYTLQGEWKFGSTLCFLLPYAQVLAVHVSTVTLNVIALDRHRCIVYHLETRMRKDVCFGVIALTWVLSAV
          .YTL..EWKFG..LC...P.AQ.L.VHVS..TL.VIAL.R.RCIV.HL..R..........A.TW..S.V
Retrocopy IYTLLDEWKFGAVLCHMVPFAQALSVHVSILTLTVIALERYRCIVFHLGRRLTWHSSLFIMAFTWTISSV

Parental  LASPMAIFREYGSFVLDP-GHTLQFCREKWP-GKGTDGTLYSISMLILQYFLPLSIISFAYARIWSKLRG
          LA.P.AIFREY......P.......C.EKWP.G...DG..YS.SM..L.Y.LPL.IIS.AY..IW.KL..
Retrocopy LAAPLAIFREYRYEEIPPINLRMPVCSEKWPHGINRDGVIYSLSMILLLYILPLAIISYAYICIWVKLKN

Parental  HVSPAESGVSSSASSERHRRRRKTTKMLVTMVVVFAVCWLPIHAFQLATDIDSSVLDMRDYRLLYTIFHV
          HVSP.....S...S..R.....K...ML...VVVFA..WLP.H..QLATD.D..VL....Y.L..T.FH.
Retrocopy HVSPS----SRNDSINRRKKTTK---MLALVVVVFATSWLPLHVLQLATDLD-LVLRFEEYKLIFTVFHI

Parental  IAMCSTFANPLLYGWMNRNYRAAFLAVFKC
          .AMC.TF.NPLLYGWMN.NYR..F..VF.C
Retrocopy VAMCPTFTNPLLYGWMNKNYRNGFIMVFRC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xmac_16 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_16 was not experimentally validated.

Homology

Retrocopy orthology:

Xiphophorus maculatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000057718	1 retrocopy	retro_drer_6,
Oreochromis niloticus	ENSONIG00000014098	1 retrocopy	retro_onil_24,
Xiphophorus maculatus	ENSXMAG00000000370	1 retrocopy	retro_xmac_12,
Xiphophorus maculatus	ENSXMAG00000008242	1 retrocopy	retro_xmac_16 ,