RetrogeneDB ID: retro_vpac_229

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3051:137505..138335(+)
• Located in intron of: ENSVPAG00000010693

Retrocopy information

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

Parental gene information

• Parental gene symbol: MORF4L1
• Ensembl ID: ENSVPAG00000008847
• Aliases: None
• Description: mortality factor 4 like 1 [Source:HGNC Symbol;Acc:16989]

Sequence

>retro_vpac_229
ATACATTACAGTGGTTGGAATAAAAATTGGCATGAGTGGGTTCCAGAAAGCAGAGTACTCAAATACGTGGACACTGATCT
GCAGAAACAATGAGAACTTCAAAAAGCCAATCAGGAGCAATATGCAGAGGGGAAGATGAGAGGGGCTGCCCCTGGAAAGA
AGACATCTGGTCTGCAACAGAAAAGTGTTGAAGAGAGAACAAACAGAAAACACCTGGAAATGGAGATGGTGGCAGTACCA
GTGGGACACCTCAGCCTCCTCGCAAGAAAAGGGCCCGAGTAGATCCTACTGTTGAAAACAAGGAAACATTCATGAACAGA
GTTGAGGTTAAAGTAAAGATTCCTGAAAAACTAAAACCATGGCTTGTTGATGATTCGGACTTAATTACCTGACAAAAACA
GCTCTTTTATCTTCCTGCCAAGAAGAATGTGGATTCCATTCTAGAGGATTATGCAAATTATAAGAAATCTTGTGGAAACA
CAGATAATAAGGAGTATGCTGTTAATGAAGTCATGGCAGGGATAAAGGAATACTTCAATGTAATGTTGGGCACTCAACTA
CTCTACAAATTTGAGAGACCACAGTATACTGAAATCCCTGCTGATCATCCTGACGCGCCCATGTCCCAGGTGTATGGAGC
GCCACATCTACTGAGATTATTTGTACGAATTGGAGCAATGTTGGCCTGTACGCCTCTGGATGAGAAGAGCCTTGCTTTAT
TACTGAATTATCTTCATGATTCCCTAGAATACCTGGCAAAGAACTCTGCAACTTTGTTTAGTGCCAGCGATTATGAAGTG
GCCCCTCCTGAGTACCATCGGAAAGCTGTG

Alignment

ORF - retro_vpac_229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.99 %
• Parental protein coverage: 80.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VHHPLLTSSWDEWVPESRVLKYVDTNLQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKT-KK
          .H.......W.EWVPESRVLKYVDT.LQKQ.ELQKANQEQYAEGKMRGAAPGKKTSGLQQK.VE..T.K.
Retrocopy IHYSGWNKNWHEWVPESRVLKYVDTDLQKQ*ELQKANQEQYAEGKMRGAAPGKKTSGLQQKSVEERT<KQ

Parental  NKQKTPGNGDGGSTSETPQPPRKKRARVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLF
          ........G....T...P...RKKRARVDPTVEN.ETFMNRVEVKVKIPE.LKPWLVDD.DLIT.QKQLF
Retrocopy KTPGNGDGGSTSGTPQPP---RKKRARVDPTVENKETFMNRVEVKVKIPEKLKPWLVDDSDLIT*QKQLF

Parental  YLPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDA
          YLPAKKNVDSILEDYANYKKS.GNTDNKEYAVNEV.AGIKEYFNVMLGTQLLYKFERPQY.EI.ADHPDA
Retrocopy YLPAKKNVDSILEDYANYKKSCGNTDNKEYAVNEVMAGIKEYFNVMLGTQLLYKFERPQYTEIPADHPDA

Parental  PMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKA
          PMSQVYGAPHLLRLFVRIGAMLA.TPLDEKSLALLLNYLHD.L.YLAKNSATLFSASDYEVAPPEYHRKA
Retrocopy PMSQVYGAPHLLRLFVRIGAMLACTPLDEKSLALLLNYLHDSLEYLAKNSATLFSASDYEVAPPEYHRKA

Parental  V
          V
Retrocopy V

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_229 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_229 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010988	1 retrocopy	retro_btau_137,
Canis familiaris	ENSCAFG00000014113	1 retrocopy	retro_cfam_20,
Callithrix jacchus	ENSCJAG00000002214	5 retrocopies	retro_cjac_2113, retro_cjac_2280, retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Felis catus	ENSFCAG00000012197	1 retrocopy	retro_fcat_75,
Loxodonta africana	ENSLAFG00000009851	1 retrocopy	retro_lafr_62,
Monodelphis domestica	ENSMODG00000011517	2 retrocopies	retro_mdom_150, retro_mdom_158,
Oryctolagus cuniculus	ENSOCUG00000015117	2 retrocopies	retro_ocun_108, retro_ocun_21,
Otolemur garnettii	ENSOGAG00000006047	4 retrocopies	retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Sarcophilus harrisii	ENSSHAG00000018402	1 retrocopy	retro_shar_393,
Ictidomys tridecemlineatus	ENSSTOG00000013294	3 retrocopies	retro_itri_111, retro_itri_1545, retro_itri_1608,
Tupaia belangeri	ENSTBEG00000001897	8 retrocopies	retro_tbel_1694, retro_tbel_1704, retro_tbel_4638, retro_tbel_518, retro_tbel_550, retro_tbel_69, retro_tbel_753, retro_tbel_76,
Tursiops truncatus	ENSTTRG00000016606	1 retrocopy	retro_ttru_472,
Vicugna pacos	ENSVPAG00000008847	1 retrocopy	retro_vpac_229 ,