RetrogeneDB ID: retro_ptro_1833

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:146026392..146027606(+)
• Located in intron of: ENSPTRG00000015483

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2AK1
• Ensembl ID: ENSPTRG00000018904
• Aliases: None
• Description: None

Sequence

>retro_ptro_1833
GGCTGCGCTGCAGCCCGCGAGCACAAAGAGGAGGGCCACGGGGTGGAGACTGTTGCTGTGCCATCTGCCATCGACTTTTC
CACCAAGAGCCTGGACTCCAAATATGACTTATGTTCCAGCAGAACTCCAGGTATTAAAATAACCCCTACAACAGCCAACT
TTCCCTTTTGCAGTTGCAAACCAGCTGCCGCTTATTTCTTTGGTGAAGCACTTGAGCCATGTGCGTGAACCAAACCCAGT
TCATTCAAGACAGGTGTTTAAGTTACTTTGCCAGACCTTTACAAAATGGGGCTGCTGTCTTCTTTCACTTGTGACAAGTT
TAGCTCATTGAGACTACATCACCACAGAGCTATTACTCACTTAATGAGGTCCACTAAAGAGAGAGTTCATCAGGATCCTT
GTGAGGCTATTTCTCATATCCAGAAAATCAGATCAAGGGAAGTACCCTTTGAAGCACAAACTTCACGTTACTTAAATGAA
TTTGAAGAACTTGCCATCTTAGGAAAAGGTGGATATGGAAGAGTATACAAGGTCAGGAATAAATTAGATGGTCAGTATTA
TGCAATTTAAAAAATCCTGATTAAGGGTGCAACAAAAACACATTACATGAAGGAACTACGGGGAATGAAGGTGCTGGCAG
GTCTTCAGCACCCTAATATTATTCGTTATCACACTGCGTGGACAGAACATGTTCAAGTGGTCCAACCACAAGCAGACAGA
GCTTCCATTCAGTTGCCATTTCTGGAAGTGTTCTCCGACCAAGCAGACAGATACCAATACGGTGTTAAAAATGGTGAAAA
TAGCAGCTCACCCATTATCTTCGCTGAGCTCACCTCAGAAAAGAAAAACCCTTTGCAGAATCTGACACTCAAAATCAGAA
TAACAAGCTGTGAACTACACCATCAATTCCGTCTTAAGAGACACCAGTGAATTTGAATCATCCCTGGAGCTCCAGGAAAA
TGGCCTGGCTGGTTTGTCTACCTGGTCAATTGTGAAACAGCCCCTGCTGCTCAGGTGTTAATTCCCTCCTAGAGGAGAAT
TTCACATCCACTGAGGAATCTTCCGAAGAAAACTTCAACTTGTTGGTGATCGAGGTGCAGTACCACCTGATGCTGCACAT
CCAGATGCAGGTGTGCAAGCTCCAGCTGTGGGACTGGCTAGCTGAGAGAAACAAACAGGGCCAAGAGTGTGTGGGCAAGT
TTGCCTGTCCTTAT

Alignment

ORF - retro_ptro_1833 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.98 %
• Parental protein coverage: 65.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GNSGVRKREEEGDGAGAVAAPPAID-FPAEGPDPKYDESDVPAELQVLKEPLQQPTFPFAVANQLLLVSL
          G....R...EEG.G...VA.P.AID.FP.....P......VPAELQVLK.PLQQPTFPFAVANQL.L.SL
Retrocopy GCAAAREHKEEGHGVETVAVPSAID>FPPRAWTPNM--TYVPAELQVLK*PLQQPTFPFAVANQLPLISL

Parental  LEHLSHVHEPNPLRSRQVFKLLCQTFIK-MGLLSSFTCSDEFSSLRLHHNRAITHLMRSAKERVRQDPCE
          ..HLSHV.EPNP..SRQVFKLLCQTF.K.MGLLSSFTC.D.FSSLRLHH.RAITHLMRS.KERV.QDPCE
Retrocopy VKHLSHVREPNPVHSRQVFKLLCQTFTK<MGLLSSFTC-DKFSSLRLHHHRAITHLMRSTKERVHQDPCE

Parental  DISHIQKIRSREVALEAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAIKKILIKGATKTVCMKV
          .ISHIQKIRSREV..EAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAI.KILIKGATKT..MK.
Retrocopy AISHIQKIRSREVPFEAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAI*KILIKGATKTHYMKE

Parental  LREVKVLAGLQHPNIVGYHTAWIEHVHVIQPRADRAAIELPSLEVLSDQEEDREHCGVKNDESSSSSIIF
          LR..KVLAGLQHPNI..YHTAW.EHV.V.QP.ADRA.I.LP.LEV.SDQ..DR...GVKN.E.SSS.IIF
Retrocopy LRGMKVLAGLQHPNIIRYHTAWTEHVQVVQPQADRASIQLPFLEVFSDQ-ADRYQYGVKNGENSSSPIIF

Parental  AEPTPE-KEKRFGESDTENQNNK-SVKYTTNLVIRDSGELESTLELQENGLAGLSASSIVEQQLPLR-RN
          AE.T.E.KEK.F.ESDT.NQNNK..V.YT.N.V.RD..E.ES.LELQENGLAGLS..SIV.Q.L.LR..N
Retrocopy AELTSE<KEKPFAESDTQNQNNK<AVNYTINSVLRDTSEFESSLELQENGLAGLSTWSIVKQPLLLR>VN

Parental  SHLEESFTSTEESSEENFNFLGQTEAQYHLMLHIQMQLCELSLWDWIVERNKRGREYVDESACPY
          S.LEE.FTSTEESSEENFN.L...E.QYHLMLHIQMQ.C.L.LWDW..ERNK.G.E.V...ACPY
Retrocopy SLLEENFTSTEESSEENFNLL-VIEVQYHLMLHIQMQVCKLQLWDWLAERNKQGQECVGKFACPY

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.80 RPM	72.23 RPM
SRP007412_cerebellum	1.15 RPM	94.39 RPM
SRP007412_heart	0.29 RPM	38.74 RPM
SRP007412_kidney	1.15 RPM	95.32 RPM
SRP007412_liver	0.49 RPM	82.92 RPM
SRP007412_testis	1.48 RPM	41.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1833 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1833 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1833 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2713

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000086232	1 retrocopy	retro_hsap_2713,
Nomascus leucogenys	ENSNLEG00000000992	1 retrocopy	retro_nleu_1586,
Pan troglodytes	ENSPTRG00000018904	1 retrocopy	retro_ptro_1833 ,