RetrogeneDB ID: retro_vpac_367

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_1277:295429..296362(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSVPAG00000001299
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]

Sequence

>retro_vpac_367
GTCAAACCCAATGCTACCACAAAGAGTTGAAAAAGGCTTACAGGAAACTGGCCTTGAAGTACCAACCTGATAAGAACCCA
AATGGAGGAGAGAAGTTTAAATACATTTGTCAAGCTTATGAAGTGCTCTTTGATGCAAACCAAAGGGAATTATTTGACAA
AGAAGGAGAACAGGCAATTAAAGAAGGCGGAGCAGGGGACAGTTTTGGCTCCCCTGTGGATATCTCTGATATGTTTTTTG
AAGGAGGAGGAAGGATGCAGAGAGAAAGGAGAGGTTAAAATGTTGTACATCAACTCTTGGTAACCTTGGAAGATTTATAT
AATGGTGCAACAAGAAAACTAGCACTGCAAAAGAATGTGATTTGTGACAAATGTGAAGGCCAAGCTGGTAAGAAAGGAGC
AGTAGAATGCTGTCCCAATTGCTGTGGTACTGCAATGCAAATAAGAATTAATCAGATAGGACCAGGAATGGTTCAGCAAA
TTCAGTCCGTATGTATGGAGTGCCAGGGCCACAGGGAGTGGATCAGTCCTAAAGACAGATGTAAAGCTGCAATGGAAGGA
AGATAGTTCGAGAGAAGATAATTCTAGAAGTTCATATTGACAAAGGCATGAAAGATGGCCAGAAGATAGCATTCTATGGT
GAAGGAGACCAAGAACTAGGACTGGAGCCAGGAGATACTATCATTGTTTTAGATCAGAAGTCCATGCTATTTTCACTTAA
CAAGAAGACTTTTTCATATGTATGGACATACAGCTGGTTGAGGCATTGTGTGGCTTCCAAAAGCCAACATCTACTATTGA
CAACTAAACAAGAGTCATCACTTCTCATGCAGGTCAGATTGCCAAGCATGGAGATATCAAGTGTGTGCTAAATGAAAGAA
TGCCAATTTATTGTAGACCATGTGAAAAGGGTCACTTAATCATTGAATTTAAG

Alignment

ORF - retro_vpac_367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.49 %
• Parental protein coverage: 78.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VKPNAT-HEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGEQAIKEGGAGGGF
          VKPNAT.H.ELKKAYRKLALKY.PDKNPN.GEKFK.I.QAYEVL.DA..REL.DK.GEQAIKEGGAG..F
Retrocopy VKPNAT<HKELKKAYRKLALKYQPDKNPNGGEKFKYICQAYEVLFDANQRELFDKEGEQAIKEGGAGDSF

Parental  GSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGRGGKKGAVECCP
          GSP.DI.DMFF.GGGRMQRERRG.NVVHQL.VTLEDLYNGATRKLALQKNVICDKCEG..GKKGAVECCP
Retrocopy GSPVDISDMFFEGGGRMQRERRG*NVVHQLLVTLEDLYNGATRKLALQKNVICDKCEGQAGKKGAVECCP

Parental  NCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCK-SCNGRKIVREKKILEVHIDKGMKDGQ
          NC.GT.MQIRI.QIGPGMVQQIQSVCMECQGH.E.ISPKDRCK.SCNGRKIVREK.ILEVHIDKGMKDGQ
Retrocopy NCCGTAMQIRINQIGPGMVQQIQSVCMECQGHREWISPKDRCK<SCNGRKIVREKIILEVHIDKGMKDGQ

Parental  KITFHGEGDQEPGLEPGDIIIVLDQKD-HAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITS
          KI.F.GEGDQE.GLEPGD.IIVLDQK..HA.FT...ED.F.CMDIQLVEALCGFQKP.ST.DN.T.VITS
Retrocopy KIAFYGEGDQELGLEPGDTIIVLDQKS<HAIFT*Q-EDFFICMDIQLVEALCGFQKPTSTIDN*TRVITS

Parental  HPGQIVKHGDIKCVLNEGMPIYRRPFEKGRLIIEFK
          H.GQI.KHGDIKCVLNE.MPIY.RP.EKG.LIIEFK
Retrocopy HAGQIAKHGDIKCVLNERMPIYCRPCEKGHLIIEFK

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_367 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_367 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 8 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Loxodonta africana	ENSLAFG00000001527	2 retrocopies	retro_lafr_1019, retro_lafr_936,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Vicugna pacos	ENSVPAG00000001299	1 retrocopy	retro_vpac_367 ,