RetrogeneDB ID: retro_apla_2

Retrocopy location

• Organism: Duck (Anas platyrhynchos)
• Coordinates: KB742522.1:909552..910686(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAPLG00000001575
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSAPLG00000010147
• Aliases: None
• Description: actin, beta [Source:HGNC Symbol;Acc:132]

Sequence

>retro_apla_2
ATGTTTGACCCCAGCGTTTTGGACGTCCCAGCAGTGATCTTTGACAACGGGTCTGGGTTATGCAAGGCAGGTGTCGCAGG
TGACAGTGGCCCAAGGTCTGTTATCACGGCAGTTGTTGGTCGCTCAAAAGCCAAATCTACAATGCTTGGAGCTGGGATGA
AAGAATACTACGTTGGAGAAGAAGCTCAGTCCAAAAGAGGGATCCTGTCTTTGAATTACCCGATTGACCATGGCATCGTT
ACCTCCTGGGATGACATGGAGAGGATCTGGAGACACGTCTACGAGCATGAGCTGAGACTCAAAGCCGCTGAAAGGCCGGT
GCTGTTGACAGAAGCCCCCCTAAATCCTCTGCAGAACCGGGAGAAAATGACAGAGATCATGTTTGAAGGCTTCATGGTGC
CCGCTATGTACGTGGCAGTCCAGGCAGCTCTGGCACTCTACGCCTCAGCCCGCACCACCGGGATCGTCATGGACAGCGGG
GACGGTGTCACCCACACGGTCCCCATTTACGAGGGGTACTGCCTGCCCCATGCTGTCTCCAGGCTGGATGTCGCTGGCAG
AGATATCACCGAGTATTTCATGAGGCTTCTTCTGGAGGGCGGGCACTCTTTTGTTAGCACAGCTGAAAGGGAAATCGTGA
GAGATATCAAAGAGAAGCTGTGCTACGTAGCTTTGGACCCCATCCAAGAAATGAAAGCAAAGCCCGAAGAAGTCATGAAA
GAGTACAGGTTACCCGACAGCAACGTCATTCAGATCGGCAGCCAGCTCTTCCGTGCTCCAGAGGTGCTCTTTGTGCCTGC
AAACATCGGCATTGAAGCACCTGGCGTGCACAAAATGATCTTCAACAGCGTCATGAAGTGCGACATCGACGTGCGCAGGA
ACCTCTACGCCAACGTCCTGCTCTCGGGAGGCTCCACGCTCTTTCCTGGACTGGAGGAGCGGATCCTGAGGGAGATGCAC
CTCCAAGTGCCCACGGGCATGTTCGTGAGGATCGTTGCCCCCCCCGAGAGAAAATACAGCGTGTGGATCGGGGCCTCCGT
CCTCACCTGCCTGACGTCTTTCAAGCAAATGTGGGTCACCGTGAGTGACTACAAGGACTTCGGGGCAGCCGTTATCCATC
GGAAGTGCTTCTGA

Alignment

ORF - retro_apla_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWD
          DNGSG.CKAG.AGD..PR.V....VGR......M.G.G.K..YVG.EAQSKRGIL.L.YPI.HGIVT.WD
Retrocopy DNGSGLCKAGVAGDSGPRSVITAVVGRSKAKSTMLGAGMKEYYVGEEAQSKRGILSLNYPIDHGIVTSWD

Parental  DMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTG
          DME.IW.H....ELR....E.PVLLTEAPLNP..NREKMT.IMFE.F..PAMYVA.QA.L.LYAS.RTTG
Retrocopy DMERIWRHVYEHELRLKAAERPVLLTEAPLNPLQNREKMTEIMFEGFMVPAMYVAVQAALALYASARTTG

Parental  IVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVA
          IVMDSGDGVTHTVPIYEGY.LPHA..RLD.AGRD.T.Y.M..L.E.G.SF..TAEREIVRDIKEKLCYVA
Retrocopy IVMDSGDGVTHTVPIYEGYCLPHAVSRLDVAGRDITEYFMRLLLEGGHSFVSTAEREIVRDIKEKLCYVA

Parental  LDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIR
          LD..QEM...A......K.Y.LPD..VI.IG...FR.PE.LF.P...G.E..G.H...FNS.MKCD.D.R
Retrocopy LDPIQEM--KAKPEEVMKEYRLPDSNVIQIGSQLFRAPEVLFVPANIGIEAPGVHKMIFNSVMKCDIDVR

Parental  KDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
          ..LYAN..LSGG.T..PG...R...E.....P..M...I.APPERKYSVWIG.S.L..L..F.QMW....
Retrocopy RNLYANVLLSGGSTLFPGLEERILREMHLQVPTGMFVRIVAPPERKYSVWIGASVLTCLTSFKQMWVTVS

Parental  EYDESGPSIVHRKCF
          .Y...G....HRKCF
Retrocopy DYKDFGAAVIHRKCF

Legend:

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

Expression

RNA-Seq

Anas platyrhynchos was not studied using RNA-Seq expression data.

ChIP-Seq

Anas platyrhynchos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_apla_2 retrocopy.

TSS

Anas platyrhynchos was not studied using FANTOM5 data.

Lab

retro_apla_2 was not experimentally validated.

Homology

Retrocopy orthology:

Anas platyrhynchos 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.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2 ,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,