RetrogeneDB ID: retro_pabe_2895

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:102452715..102453590(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK1IP1L
• Ensembl ID: ENSPPYG00000005836
• Aliases: None
• Description: MAPK-interacting and spindle-stabilizing protein-like [Source:UniProtKB/Swiss-Prot;Acc:Q5R623]

Sequence

>retro_pabe_2895
GAGGAGGAGCCGCGCACTGCTGGTGCTGTTGCCGCGCTGCTCTCGCTGCAGTCAGTCAGGCTGTGCCCGCTTCTTCAGGG
CCCAGTCCCTTGGACCCATCGCCACTTCTAGACCCTACTGCAGTCTTGGATATTGCCGGGAAAATGTCTGATGAATTTTC
GTTGGCAGATGCACTACCTGAACACTCCCCTGCCAAAACCTCTGCTGTGAGCAATACAAAACCTGGCCAACCTCCTCAAA
GCTGACCAGGCTCCAACCCTTGGAATAATGCGAGTGCTCCACCTTCGGTGCCATCTGGACCCCCACCAAGTGCAACACCC
TCCACTGTGCCTTTTGGACCAGTACCAACAGGAATGTATCTCTCCGTGCCTCCCACCGGACCACCTCCAGGACCCCCAGC
ACCCTTTACTCCTTCTGGACCATCATGCCCCCCACCTGGTGGTCCTTATCCAGCCCCAACTGTGCCAGGCCCTGGCCCCA
TAGGGCCATATCCTACACCAAATATGCCCTTTCCAGAGCTACCCAGACCATATGGTGCACCCACAGATCCAGCTGCAGCT
GGTCCTTTAGGTCCATGGGCATCCATGTCTTCTGGACCTTGGGTGCCAGGAATGGGAGGGCAGTATCCTACCCCTAATAT
GCCATATCCATCTCCAGGGCCATATCCCATTCCTCCTCCTCCCCAAGCCTCTGGGGCAGCACCACCTGTTCCATGGGGCA
CCGTTCCACTAGGAGCCTGGGGACCACCAGCACCATATCCTGCCCCTACAGGATGGTATGCCACACCAGGACTCTATCCT
ACTCCCAGTAATCCTTTCCAAGTGCCTTCAGGACCTTCTGGTACTCCACCGATGCCTGGTGGCCCCCATTCTTAC

Alignment

ORF - retro_pabe_2895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 97.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QEEPRAAGAVAA-AALAAISQAAPVSSGPSPSDPSPLLDPTAVSDIAGKMSDEFSLADALPEHSPAKTSA
          .EEPR.AGAVAA.AALAA.SQA.P.SSGPSP.DPSPLLDPTAV.DIAGKMSDEFSLADALPEHSPAKTSA
Retrocopy EEEPRTAGAVAA<AALAAVSQAVPASSGPSPLDPSPLLDPTAVLDIAGKMSDEFSLADALPEHSPAKTSA

Parental  VSNTKPGQPPQGWPGSNPWNNPSAPSSVPSGLPPSATPSTVPFGPAPTGMYPSVPPTGPPPGPPAPFPPS
          VSNTKPGQPPQ..PGSNPWNN.SAP.SVPSG.PPSATPSTVPFGP.PTGMY.SVPPTGPPPGPPAPF.PS
Retrocopy VSNTKPGQPPQS*PGSNPWNNASAPPSVPSGPPPSATPSTVPFGPVPTGMYLSVPPTGPPPGPPAPFTPS

Parental  GPSCPPPGGPYPAPTVPGPGPTGPYPTPNMPFPELPRPYGAPTDPAAAGPLGPWGSMSSGPWAPGMGGQY
          GPSCPPPGGPYPAPTVPGPGP.GPYPTPNMPFPELPRPYGAPTDPAAAGPLGPW.SMSSGPW.PGMGGQY
Retrocopy GPSCPPPGGPYPAPTVPGPGPIGPYPTPNMPFPELPRPYGAPTDPAAAGPLGPWASMSSGPWVPGMGGQY

Parental  PTPNMPYPSPGPYPAPPPPQAPGAAPPVPWGTVPPGAWGPPAPYPAPTGSYPTPGLYPTPSNPFQVPSGP
          PTPNMPYPSPGPYP.PPPPQA.GAAPPVPWGTVP.GAWGPPAPYPAPTG.Y.TPGLYPTPSNPFQVPSGP
Retrocopy PTPNMPYPSPGPYPIPPPPQASGAAPPVPWGTVPLGAWGPPAPYPAPTGWYATPGLYPTPSNPFQVPSGP

Parental  SGAPPMPGGPHSY
          SG.PPMPGGPHSY
Retrocopy SGTPPMPGGPHSY

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	2.49 RPM	22.67 RPM
SRP007412_cerebellum	2.92 RPM	39.16 RPM
SRP007412_heart	1.84 RPM	22.16 RPM
SRP007412_kidney	4.11 RPM	32.42 RPM
SRP007412_liver	1.87 RPM	20.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2895 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2895 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2895 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000012787	1 retrocopy	retro_nleu_794,
Oryctolagus cuniculus	ENSOCUG00000004003	1 retrocopy	retro_ocun_1030,
Pongo abelii	ENSPPYG00000005836	2 retrocopies	retro_pabe_2895 , retro_pabe_881,