RetrogeneDB ID: retro_vpac_652

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_96649:576..1460(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP4
• Ensembl ID: ENSVPAG00000011876
• Aliases: None
• Description: retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]

Sequence

>retro_vpac_652
GGAGGTTTTGGCTCAGTTAGTGGAAAAACTGAAATAGAAATCAAGATCAACCATAAAGGAGAAGTAAACAGGGCACATTA
TATGCCCCAGAACCCTTGCATCATTGCAACAAAGACTCCATCCAGTGATGTTCTTGTTTTTGACTATACGAAACATCCTT
CTAAACCAGACCCTTCTGGAGAGTGCAACCCAGACTTGCATCTCCGTGGACATCAGAAGGAAGGCTATGGGCTTTCTTGG
AACCCAAATCTCAGTGGGCACTTACTTAGTGCTTCAGATGACCATACCATCTGCCTGTGGGACATCAGTGCTGTTCCAAA
GGAAGGAAAAGTTGTGGACGCAAAGACCATCTTTACAGGGCATACAGCAGTCTCTTGGCATCTGCTCCATGAGTCTCTGT
TTGGATCAGTTGCTGATGATCAGAAGCTTACAATCTGGGATACTCGTTCAAACAATTCTTCCAAACCAAGCCACTCAGCT
GATGCTCACCCTGCTGAAGTGAACTGCCTTTCTTTCAATCCGTATAGTGAGTTCATTCTTGCCACAGGATCAGCTGACAA
GACTGTTGCCTTGTGGGATCTGAGAAATCCGAAAACTGAAGTTGCATTCCTTTGAATCACATAAGGATGAAACATTCCAG
GCTCAGTGGTCACCTCACAATGAGACTAGTTTGGCTTCCAGGGGTACCGATCACAGACTGAACACCTGGAAAGTAAGTAA
AACTGGAGAGGAACAATCCCCAGAAGATGCAGAAGATGGGCCACCAGAGTTGTTTAATCACGGTGGTAACACTTTCCAAG
ATATCTGATTTCTTCTAGAATCCCAATGCATCTTGGGTGATTGGTTCTGTATCAGAAGCCAGTATCATGCAACTGTGGGA
AATG

Alignment

ORF - retro_vpac_652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.71 %
• Parental protein coverage: 70.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRG
          GGFGSVSGK.EIEIKINH.GEVNRA.YMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDL.LRG
Retrocopy GGFGSVSGKTEIEIKINHKGEVNRAHYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLHLRG

Parental  HQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGS
          HQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAV....SWHLLHESLFGS
Retrocopy HQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAV----SWHLLHESLFGS

Parental  VADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRN-LKLKLHSFE
          VADDQKL.IWDTRSNN.SKPSHS.DAH.AEVNCLSFNPYSEFILATGSADKTVALWDLRN..KLKLHSFE
Retrocopy VADDQKLTIWDTRSNNSSKPSHSADAHPAEVNCLSFNPYSEFILATGSADKTVALWDLRN>RKLKLHSFE

Parental  SHKDEIFQXQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHT-AKISDFSWN
          SHKDE.FQ.QWSPHNET.LAS.GTD.RLN.W..SK.GEEQSPEDAEDGPPE.LF.HGG.T..KISDF..N
Retrocopy SHKDETFQAQWSPHNETSLASRGTDHRLNTWKVSKTGEEQSPEDAEDGPPE-LFNHGGNT>SKISDFF*N

Parental  PNEPWVICSVSEDNIMQVWQM
          PN..WVI.SVSE..IMQ.W.M
Retrocopy PNASWVIGSVSEASIMQLWEM

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_652 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_652 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001021	7 retrocopies	retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus	ENSCPOG00000015352	3 retrocopies	retro_cpor_154, retro_cpor_27, retro_cpor_899,
Gorilla gorilla	ENSGGOG00000011313	4 retrocopies	retro_ggor_1022, retro_ggor_1314, retro_ggor_1867, retro_ggor_2428,
Macaca mulatta	ENSMMUG00000009940	1 retrocopy	retro_mmul_75,
Mustela putorius furo	ENSMPUG00000015214	1 retrocopy	retro_mputfur_104,
Otolemur garnettii	ENSOGAG00000011632	2 retrocopies	retro_ogar_3079, retro_ogar_3297,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Rattus norvegicus	ENSRNOG00000021492	1 retrocopy	retro_rnor_1270,
Sarcophilus harrisii	ENSSHAG00000010923	1 retrocopy	retro_shar_399,
Tupaia belangeri	ENSTBEG00000002236	3 retrocopies	retro_tbel_1360, retro_tbel_1718, retro_tbel_3802,
Vicugna pacos	ENSVPAG00000011876	4 retrocopies	retro_vpac_333, retro_vpac_419, retro_vpac_652 , retro_vpac_94,