RetrogeneDB ID: retro_cjac_947

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:123410908..123411808(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031574
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PLEKHA1
• Ensembl ID: ENSCJAG00000001251
• Aliases: None
• Description: pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1 [Source:HGNC Symbol;Acc:14335]

Sequence

>retro_cjac_947
ATGCCTTATGTGGATCGTCAGAATCGCATTTGTGGTTTTCTAGACATTGAAGAAAATGAAAACAGTGGGAAATTTCTTCG
AAGGTACTTCATACTGGATACCAGAGAAGATAGTTTCGTGTGGTACATGGATAATCCACAGAACCTACCTTCTGGATCAT
CACGTGTTGGAGCCATTAAACTTACCTACATTTCAAAGGTTAGCGATGCTACTAAGCTGAGGCCAAAGGCTGAGTTCTGT
TTTGTTATGAATGCAGGAATGAGGAAGTACTTCCTACAAGCCAATGATCAGCAGGACCTAGTGGAATGGGTAAATGTGTT
AAACAAAGCTATAAAAATTACAGTACCAAAGCAGTCAGACTCACAGCCTAATTCTGATAACCTAAGTCGCCATGGTGAAT
GTGGGAAGAAGCAAGTGTCTTACAGAACTGATATTGTTGGTGGCGTACCCATCATTACTCCCACTCAGAAAGAAGAAGTA
AATGAATGTGGTGAAAGTATTGACAGAAATCATCTGAAACGGTCACAAAGCCATCTCCCTTACTTTGCTCCTAAACCACC
TCTGGATAGTGCAGTTATCAAAGCTGGATATTGTGTCAAGCAAGGAGCTGTGATGAAAAACTGGAAGAGAAGATATTTTC
AGTTGGATGAAAACACAATAGGCTACTTCAAATCTGAACTGGGAAAGGAACCTCTTCGTATTATTCCACTTAAAGAGGTT
CATAAAGTCCAGGAATGTAAGCAAAGTGACATAATGATGAGGGACAACCTCTTTGAAATTGTAACAACGTCTCGAACTTT
CTACGTGCAGGCTGATAGCCCTGAAGAGATGCACAGCTGGATTAAAGCAGTCTCTGGCGCCATCGTAGCACAGCGGGGGC
CCGGCAGATCTGCGTCTTCT

Alignment

ORF - retro_cjac_947 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.33 %
• Parental protein coverage: 82.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPYVDRQNRICGFLDIEENENSGKFLRRYFILDTREDSFVWYMDNPQNLPSGSSRVGAIKLTYISKVSDA
          MPYVDRQNRICGFLDIEENENSGKFLRRYFILDTREDSFVWYMDNPQNLPSGSSRVGAIKLTYISKVSDA
Retrocopy MPYVDRQNRICGFLDIEENENSGKFLRRYFILDTREDSFVWYMDNPQNLPSGSSRVGAIKLTYISKVSDA

Parental  TKLRPKAEFCFVMNAGMRKYFLQANDQQDLVEWVNVLNKAIKITVPKQSDSQPNSDNLSRHGECGKKQVS
          TKLRPKAEFCFVMNAGMRKYFLQANDQQDLVEWVNVLNKAIKITVPKQSDSQPNSDNLSRHGECGKKQVS
Retrocopy TKLRPKAEFCFVMNAGMRKYFLQANDQQDLVEWVNVLNKAIKITVPKQSDSQPNSDNLSRHGECGKKQVS

Parental  YRTDIVGGVPIITPTQKEEVNECGESIDRNHLKRSQSHLPYFAPKPPLDSAVIKAGYCVKQGAVMKNWKR
          YRTDIVGGVPIITPTQKEEVNECGESIDRNHLKRSQSHLPYFAPKPPLDSAVIKAGYCVKQGAVMKNWKR
Retrocopy YRTDIVGGVPIITPTQKEEVNECGESIDRNHLKRSQSHLPYFAPKPPLDSAVIKAGYCVKQGAVMKNWKR

Parental  RYFQLDENTIGYFKSELEKEPLRVIPLKEVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSW
          RYFQLDENTIGYFKSEL.KEPLR.IPLKEVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSW
Retrocopy RYFQLDENTIGYFKSELGKEPLRIIPLKEVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSW

Parental  IKAVSGAIVAQRGPGRSASS
          IKAVSGAIVAQRGPGRSASS
Retrocopy IKAVSGAIVAQRGPGRSASS

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
SRP051959_colon	0.53 RPM	5.10 RPM
SRP051959_heart	0.58 RPM	6.07 RPM
SRP051959_kidney	0.69 RPM	9.25 RPM
SRP051959_liver	0.37 RPM	5.89 RPM
SRP051959_lung	0.76 RPM	7.26 RPM
SRP051959_lymph_node	0.53 RPM	5.00 RPM
SRP051959_skeletal_muscle	0.46 RPM	3.71 RPM
SRP051959_spleen	0.36 RPM	4.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_947 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_947 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001251	1 retrocopy	retro_cjac_947 ,
Otolemur garnettii	ENSOGAG00000010036	1 retrocopy	retro_ogar_141,
Sus scrofa	ENSSSCG00000010702	1 retrocopy	retro_sscr_416,
Tarsius syrichta	ENSTSYG00000004811	1 retrocopy	retro_tsyr_1190,