RetrogeneDB ID: retro_apla_14

Retrocopy location

• Organism: Duck (Anas platyrhynchos)
• Coordinates: KB745253.1:117790..118473(+)
• Located in intron of: ENSAPLG00000015132

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSAPLG00000011011
• Aliases: None
• Description: inositol polyphosphate multikinase [Source:HGNC Symbol;Acc:20739]

Sequence

>retro_apla_14
GGTATTCTGCAGCATCTGGATAGGACTGTCTTGAGCGGCTGCAGCGATCATCTTGAGGTCCCAGGGAGAAGGATATCTAC
AACAAGGTTTATGATGCTGACTGTTACAACAGCTTTCTTCTGGAGCTGCAAAAATATCTTCCAAAGTAATTCCATATCTG
GTCACCACCTACTGCACCAAATGATACGTATCTAAAACCAGAAGTTATGATGTATAAGTTTTACAAGCCTTGCATAATGG
ATGTAAAAATAGGGCAGAAAAATTATGATTTATATGCTTCAGCTGAGAAGATACAGCAGCAGGTCTGCAAGTACTCACTG
ATGGAAGAGCTTGGATTTTTGGTAGTGGACATGAGGGTTTACCACATCTGACAGCTATGAGACAGAAAATCAGCACTATG
GAATGAGCTTGGCAAACGAAACAGTAAAGGATGGCATTTCAAAGTTTTTCTACAATTGGTATTGCTTGAAAAAGATGTGA
TCACTGCCAGCATTCAGAAGATCGACAAAATTTTGAGGTGATTTGAGGACCAGAAACAACTCAACTTGTTTTGCTCGTTA
CCAGTTGTTTACAAAGTTTCATGTCAGGCAACAACCATGCACTTCAGTAATGACACCTTGGCAGAAAAAAGGGGAGTGCC
CAAAGGACTGTTATCAGGTGGAGACATACTTTAGTATAATAAT

Alignment

ORF - retro_apla_14 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.95 %
• Parental protein coverage: 64.53 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GILQHPDGTVL-KQLQPPPRGPREQEFYNKVYDSDCCDSILLELREYLPKYFGVWSPPTAPNEMYLKLED
          GILQH.D.TVL...LQ....GPRE...YNKVYD.DC..S.LLEL..YLPK.F..WSPPTAPN..YLK.E.
Retrocopy GILQHLDRTVL<ERLQRSS*GPREKDIYNKVYDADCYNSFLLELQKYLPK*FHIWSPPTAPNDTYLKPEV

Parental  VTRKFNKPCIMDVKIGQKSYDPYASAEKIQQQVSKYPLMEEIGFLVLGMRVYHV-SSDSYETQNQHYGRG
          ...KF.KPCIMDVKIGQK.YD.YASAEKIQQQV.KY.LMEE.GFLV..MRVYH...S...E.Q...YG..
Retrocopy MMYKFYKPCIMDVKIGQKNYDLYASAEKIQQQVCKYSLMEELGFLVVDMRVYHI>DSYETENQH--YGMS

Parental  LTKETVKDGIAKFFHNGYCLR-KDAIAASIQKIEKILAWFEGQKQLNFYASSLLFVYEGSCQATTVRLSD
          L..ETVKDGI.KFF.N.YCL..KD.I.ASIQKI.KIL..FE.QKQLN....SL..VY..SCQATT...S.
Retrocopy LANETVKDGISKFFYNWYCLK<KDVITASIQKIDKILR*FEDQKQLNLFC-SLPVVYKVSCQATTMHFSN

Parental  VTLAEKRGVPKGLLSGGDILEYNN
          .TLAEKRGVPKGLLSGGDIL.YNN
Retrocopy DTLAEKRGVPKGLLSGGDIL*YNN

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_14 retrocopy.

TSS

Anas platyrhynchos was not studied using FANTOM5 data.

Lab

retro_apla_14 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000011011	1 retrocopy	retro_apla_14 ,
Cavia porcellus	ENSCPOG00000000222	1 retrocopy	retro_cpor_369,
Erinaceus europaeus	ENSEEUG00000009958	1 retrocopy	retro_eeur_110,
Homo sapiens	ENSG00000151151	2 retrocopies	retro_hsap_1244, retro_hsap_2032,
Gorilla gorilla	ENSGGOG00000008790	1 retrocopy	retro_ggor_1464,
Myotis lucifugus	ENSMLUG00000015030	1 retrocopy	retro_mluc_518,
Nomascus leucogenys	ENSNLEG00000012319	2 retrocopies	retro_nleu_2419, retro_nleu_2622,
Pongo abelii	ENSPPYG00000002433	3 retrocopies	retro_pabe_1035, retro_pabe_1086, retro_pabe_1689,
Pan troglodytes	ENSPTRG00000002516	2 retrocopies	retro_ptro_1351, retro_ptro_855,