RetrogeneDB ID: retro_pabe_881

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:108694239..108694885(+)
• 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_881
GCACCCAGTTGTCTCAAACCCTTTGCCACTTCTACTGCAGACTAGGATCTTGCCAGGAAAATGTCTGATGAATTTTCTAT
GGCAAATGCTCTACCCGAACACTTCCCTGACCAAGTCCTGCTGTGATTAATAGAAATCTAGTCAACCTCCTTAAGGCCGG
CCAGATTCCAAACCTAGGAAGAACCCATGTGCTGTGCCTTCTATGCCATCTGGACTCCCACCAAGTGCAACACTCTTCAT
TGTACCTTTCGGACCTTTGCTAACAGGATTGCATCCCTCTGTGCCTCCCACTGGACTGCCTCTGAGGACCCGAGAACTCT
TCCTCTTTCTGGACCATCCTGCTCCCCACCTAATGGTCCTTATCCAACTTCAACTGTGATGCACCTGGACCCCACAGGCC
ATATCCTATGCCAAAAATGCCCTTTCTAGAGCTTCCCAGACCATATGGTGCTCTCACAGGTCTCACAAGTCGTGCTGCAA
CTGGTATTTTAGGTCCATGAAAATCCACATTTCTGAACCATGGGCACCAGAAATGAGAAGGCAGCATCCTACTCTAAACA
TGCCACATGTACATCTAGAGCCATATCTTACTCATCCTCCTCCAGGCACCAGGGCAGTGTCACCTTTTCCAGTGGGGCTC
TGTCCT

Alignment

ORF - retro_pabe_881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.16 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SPSDPSPLLDPTAVSDIAGKMSDEFSLADALPEHSPAK-TSAVSNT-KPGQPPQGWPGSNPWNNPSAPSS
          .PS...P....TA..D.A.KMSDEFS.A.ALPEH.P.....AV.N..K..QPP.G.P.S.P..NP.A..S
Retrocopy APSCLKPFATSTAD*DLARKMSDEFSMANALPEHFPDQ<SPAVINR<KSSQPP*GRPDSKPRKNPCAVPS

Parental  VPSGLPPSATPSTVPFGPAPTGMYPSVPPTGPP-PGPPAPFPPSGPSCPPPGGPYPAPTV-PGPGPTGPY
          .PSGLPPSAT...VPFGP..TG..PSVPPTG.P....P...P.SGPSC.PP.GPYP..TV...PGP..PY
Retrocopy MPSGLPPSATLFIVPFGPLLTGLHPSVPPTGLP<SEDPRTLPLSGPSCSPPNGPYPTSTV<DAPGPHRPY

Parental  PTPNMPFPELPRPYGAPT---DPAAAGPLGPWGSM-SSGPWAPGMGGQYPTPNMPYPSPGPYPAPPPPQA
          P.P.MPF.ELPRPYGA.T.....AA.G.LGP..S...S.PWAP.M..Q.PT.NMP.....PY...PPP..
Retrocopy PMPKMPFLELPRPYGALTGLTSRAATGILGP*KST<ISEPWAPEMRRQHPTLNMPHVHLEPYLTHPPP-G

Parental  PGAAPPVPWGTVP
          ..A..P.P.G..P
Retrocopy TRAVSPFPVGLCP

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	0.00 RPM	22.67 RPM
SRP007412_cerebellum	0.00 RPM	39.16 RPM
SRP007412_heart	0.03 RPM	22.16 RPM
SRP007412_kidney	0.00 RPM	32.42 RPM
SRP007412_liver	0.00 RPM	20.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_881 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_881 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_881 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 ,