RetrogeneDB ID: retro_pabe_1288

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:38056036..38056762(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000006379
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HTATIP2
• Ensembl ID: ENSPPYG00000003421
• Aliases: None
• Description: HIV-1 Tat interactive protein 2, 30kDa [Source:HGNC Symbol;Acc:16637]

Sequence

>retro_pabe_1288
GTGGCCGATACAGAAGCACTGTCGAAGCTTCGGGAAGACTTCAGGATGCAGAATAAATCCGTCTTTATTTTGGGCGCCAG
CAGAGAAATCGGCAGAGTGCTCTTAAAGGAAATCCTGGAGCAGGGCCTGTTTTCCAAAGTAACGCTCATTGGCCGGAGGA
AGCTCACCTTCGACGAGCAAGCTTATAAAAAATGTGAATCAAGAAGTGGTGGACTTTGAAAAGTTGGATGACTACGCTTC
TGCCTTTCAAGGTCATGATGTTGGATTCTGTTGCCTGGGTACCACCAGAGTGAAAGCTGGGGCGGAGGGATTTGTTCGTG
TTGACCGAGATTATGTGCTGAAGTCCGCAGAGCTGGCAAAAGCTGGAGGGTGCAAACATTTCAACTTGCTATCCTCTAAA
AGAGCTGATAAGTCAAGCAATTTTTTATATCTACAAGTTAAGGGAGAAGTAGAAGCCAAGGTTAAAGAATTAAAATTTGA
TCGTTACTCTGTATTTAGGCCTGGAGTTCTGTTATGTGATAGGCAAGAATCCCGCCCAGGTGAATGGTTGGTTAGAAAGT
TCTTTGGCACCTTACCAGAATCTTGGGCCAGTGGGCGTTCTGTGCTTGTGGTGACTGTGGTTAGAGCAATGCTGAACAAT
GTGGTGAGACCAAGCGACAAGCAGATGGAACTGCTGGAGAACAAGGCCATCCATGACCTGGGGAAAGTGCATGGCTCCTC
AAGCCA

Alignment

ORF - retro_pabe_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAETEALSKLREDFRMQNKSVFILGASGETGRVLLKEILEQGLFSKVTLIGRRKLTFDEEAYK-NVNQEV
          .A.TEALSKLREDFRMQNKSVFILGAS.E.GRVLLKEILEQGLFSKVTLIGRRKLTFDE.AYK.NVNQEV
Retrocopy VADTEALSKLREDFRMQNKSVFILGASREIGRVLLKEILEQGLFSKVTLIGRRKLTFDEQAYK>NVNQEV

Parental  VDRFEKLDDYASAFQGHDVGFCCLGTTRVKAGAEGFVRVDRDYVLKSAELAKAGGCKHFNLLSSKGADKS
          VD.FEKLDDYASAFQGHDVGFCCLGTTRVKAGAEGFVRVDRDYVLKSAELAKAGGCKHFNLLSSK.ADKS
Retrocopy VD-FEKLDDYASAFQGHDVGFCCLGTTRVKAGAEGFVRVDRDYVLKSAELAKAGGCKHFNLLSSKRADKS

Parental  SNFLYLQVKGEVEAKVEELKFDRYSVFRPGVLLCDRQESRPGEWLVRKFFGSLPESWASGYSVPVVTVVR
          SNFLYLQVKGEVEAKV.ELKFDRYSVFRPGVLLCDRQESRPGEWLVRKFFG.LPESWASG.SV.VVTVVR
Retrocopy SNFLYLQVKGEVEAKVKELKFDRYSVFRPGVLLCDRQESRPGEWLVRKFFGTLPESWASGRSVLVVTVVR

Parental  AMLNNMVRPRDKQMELLENKAIHDLGKVHGS-LKP
          AMLNN.VRP.DKQMELLENKAIHDLGKVHGS.LKP
Retrocopy AMLNNVVRPSDKQMELLENKAIHDLGKVHGS<LKP

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	3.04 RPM	1.77 RPM
SRP007412_cerebellum	3.65 RPM	2.07 RPM
SRP007412_heart	1.29 RPM	0.84 RPM
SRP007412_kidney	5.77 RPM	3.35 RPM
SRP007412_liver	8.02 RPM	3.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1288 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1288 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006718	1 retrocopy	retro_cjac_967,
Loxodonta africana	ENSLAFG00000018703	1 retrocopy	retro_lafr_244,
Oryctolagus cuniculus	ENSOCUG00000000749	1 retrocopy	retro_ocun_822,
Pongo abelii	ENSPPYG00000003421	1 retrocopy	retro_pabe_1288 ,
Ictidomys tridecemlineatus	ENSSTOG00000011216	2 retrocopies	retro_itri_1354, retro_itri_1523,