RetrogeneDB ID: retro_vpac_369

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_1301:2531..3292(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000007637
• Aliases: None
• Description: None

Sequence

>retro_vpac_369
CTGGTTGTGAAACAACTAATTGCTGGTGTTAACAAAATGGATTCTACAGAGCTGCTCCTCAGCCAGAGAGATAATGAGGA
AATGGTTAAGGAAGTCAACACCTACATTAAGAATATTGGCTACAACCCAGACACAGTAGCATTTGTGCCAATTTCTGGTT
GGAATGGAGACAACATGCTGGAGCCAGTTACAAATACGCCTTGGTTCAAGGGGTCAGAAGCCACCCATAGAGATGGAAAT
GCCAGTGGAACCAGACTACTCAAATCTCTTGATCTCATCCTGCCACCAGTTCTTTGAACTGTAAGGCCCTTGGATTTGTT
CCTCCAGGATGTCTACAAAATTGGTGGCATTGGTACTGTCCCTGTGGGTCGAGTGGAGACTGGTGTTATCAAACACACAT
GGTGGTCACCTTTGCTGCAGTCAATGTTACCGTTGAAGTAAAATCTGTTGAAATGCACCATGGAGTTCTGAGTGAAGCTC
TTCTTAGAGACAATGTGGGCTGCAATGTCAAGAGTGTGTCTGTCAGAGATGTTCATCATGGCATAGCAGTCAGCAATAGC
AAAAATGATCCACCAAATGGAAGCAGCTGCCTTCGTTAGTCAGGCAATTACCCTGAACCTCCCAGGCCAAATCAGTGCTG
GCTATGACCTGTGCTAGATTGTGACACAGCTCACATTGCTTGCAGGTTTACTGAGCCGAGGGAGAAGATTGATCACTATT
CTGGTAAGAAGCTGAAAGACGACCTCAAATTCTTGAAATCT

Alignment

ORF - retro_vpac_369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.15 %
• Parental protein coverage: 54.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPWFK
          L.VKQLI.GVNKMDSTE...SQ...EE.VKEV.TYIK.IGYNPDTVAFVPISGWNGDNMLEP..N.PWFK
Retrocopy LVVKQLIAGVNKMDSTELLLSQRDNEEMVKEVNTYIKNIGYNPDTVAFVPISGWNGDNMLEPVTNTPWFK

Parental  GWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLK-PGMVVTFA
          G...T..DGNASGT.LL..LD.ILPP...T..PL.L.LQDVYKIGGIGTVPVGRVETGV.K...MVVTFA
Retrocopy GSEATHRDGNASGTRLLKSLDLILPPVL*TVRPLDLFLQDVYKIGGIGTVPVGRVETGVIK<THMVVTFA

Parental  PVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPP-MEAAGFTAQVIILNHP
          .VNVT.EVKSVEMHH..LSEAL..DNVG.NVK.VSV.DV..G.....SKNDPP.MEAA.F..Q.I.LN.P
Retrocopy AVNVTVEVKSVEMHHGVLSEALLRDNVGCNVKSVSVRDVHHGIAVSNSKNDPP>MEAAAFVSQAITLNLP

Parental  GQISAGYA-PVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKS
          GQISAGY..PVLDC.TAHIAC.F.E..EKID..SGKKL.D..KFLKS
Retrocopy GQISAGYD<PVLDCDTAHIACRFTEPREKIDHYSGKKLKDDLKFLKS

Legend:

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

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_369 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_369 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos 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 11 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Cavia porcellus	ENSCPOG00000004067	15 retrocopies	retro_cpor_1150, retro_cpor_1162, retro_cpor_1191, retro_cpor_1256, retro_cpor_1393, retro_cpor_1492, retro_cpor_1499, retro_cpor_348, retro_cpor_381, retro_cpor_387, retro_cpor_413, retro_cpor_709, retro_cpor_891, retro_cpor_918, retro_cpor_959,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Vicugna pacos	ENSVPAG00000007637	9 retrocopies	retro_vpac_369 , retro_vpac_404, retro_vpac_510, retro_vpac_511, retro_vpac_523, retro_vpac_544, retro_vpac_582, retro_vpac_592, retro_vpac_606,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,