RetrogeneDB ID: retro_hsap_3018

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:189659526..189660645(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000180015
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTRF1L
• Ensembl ID: ENSG00000112031
• Aliases: MTRF1L, HMRF1L, MRF1L, mtRF1a
• Description: mitochondrial translational release factor 1-like [Source:HGNC Symbol;Acc:21051]

Sequence

>retro_hsap_3018
GGCGCTGCCCGGTGGCTCTGGCCCCGCCGGGCCGTTGGCCCAGCCCGCCGGCCCCTGAGCTCCGGTAGCCCGCCGCTGGA
GAAGCTGTTCGCCCGGGGCGGGCCCTTGCGGACCTTCCTCGAGCGCCAGGCGGGGTCTGAAGCCCATTTGAAGGTCAGGA
GGCCCGAGTTGCTGGCGGTGATCAAACTGCTGAACGAGAAGGAGCAGGAGCTGCGGGAGACTGAGCACTTGCTGCACGAT
GAGAATGAAGGTTTAAGGAAACTTGCAGAGAATGAAATCACTTTGTGTCAAAAAGAAATAACTCAGCTGAAGCATCAGAT
TATCTTACTTTTGGTTCCCTCAGAAGAAACAGATGAAAATGATTTGATCCTGGAAGTAACTGCAGGAGTTGGAGGTCAGG
AGGCAATGTTGTTTACATCAGAGATATTTGATATGTATCAGCAATATGCTGCATTTAAAAGATGGCATTTTGAAACCCTG
GAATATTTTCCAAGTGAAGTAGGTGGCCTTAGACATGCATCTGCCAGCATTGGGGGTTCAGAAGCCTATAGGCACATGAA
ATTTGAAGGAGGTGTTCACAGAGTACAAAGAGTGCCAAAGACAGAAAAGCAAGGCTGCGTCCATACTAGCACCATGACTG
TAGCAATATTACCCCAGCCTACTGAGATTAATCTGGTGATTAATCCGAAAGATTTGAGAATTGACACTAAGCGAGCCAGT
GGAGCTGGGGAGCAGCATGTAAATACCACGGACAGTGCTGTCCGGATAGTTCATCTTCCAACAGGTGTTGTTTCTGAATG
TCAACAAGAGAGATCTCAGCTGAAAAATAAAGAGCTGGCTATGACAAAGTTACGTGCAAAACTGTACAGCATGCATGTAG
AAGAAGAAATAAATAAAAGACAGAATGCTAGAAAAATTCAGATTGGAAGTAAAGGAAGATCAGAGAAAATAAGAACATAT
AATTTTCCACAGAACCGGGTCACAGATCACAGAATAAACAAGACGCTGCATGATCTTGAAACTTTTATGCAAGGAGATTA
TCTACTGGATGAACTTGTACAGTCATTGAAGGAATACGCCAATTATGAATCTTTAGTAGAAATTATTTCCCAAAAAGTT

Alignment

ORF - retro_hsap_3018 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.59 %
• Parental protein coverage: 98.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAARWLWPRRAVGPARRPLSSGSPPLEELFTRGGPLRTFLERQAGSEAHLKVRRPELLAVIKLLNEKERE
          GAARWLWPRRAVGPARRPLSSGSPPLE.LF.RGGPLRTFLERQAGSEAHLKVRRPELLAVIKLLNEKE.E
Retrocopy GAARWLWPRRAVGPARRPLSSGSPPLEKLFARGGPLRTFLERQAGSEAHLKVRRPELLAVIKLLNEKEQE

Parental  LRETEHLLHDENEDLRKLAENEITLCQKEITQLKHQIILLLVPSEETDENDLILEVTAGVGGQEAMLFTS
          LRETEHLLHDENE.LRKLAENEITLCQKEITQLKHQIILLLVPSEETDENDLILEVTAGVGGQEAMLFTS
Retrocopy LRETEHLLHDENEGLRKLAENEITLCQKEITQLKHQIILLLVPSEETDENDLILEVTAGVGGQEAMLFTS

Parental  EIFDMYQQYAAFKRWHFETLEYFPSELGGLRHASASIGGSEAYRHMKFEGGVHRVQRVPKTEKQGRVHTS
          EIFDMYQQYAAFKRWHFETLEYFPSE.GGLRHASASIGGSEAYRHMKFEGGVHRVQRVPKTEKQG.VHTS
Retrocopy EIFDMYQQYAAFKRWHFETLEYFPSEVGGLRHASASIGGSEAYRHMKFEGGVHRVQRVPKTEKQGCVHTS

Parental  TMTVAILPQPTEINLVINPKDLRIDTKRASGAGGQHVNTTDSAVRIVHLPTGVVSECQQERSQLKNKELA
          TMTVAILPQPTEINLVINPKDLRIDTKRASGAG.QHVNTTDSAVRIVHLPTGVVSECQQERSQLKNKELA
Retrocopy TMTVAILPQPTEINLVINPKDLRIDTKRASGAGEQHVNTTDSAVRIVHLPTGVVSECQQERSQLKNKELA

Parental  MTKLRAKLYSMHLEEEINKRQNARKIQIGSKGRSEKIRTYNFPQNRVTDHRINKTLHDLETFMQGDYLLD
          MTKLRAKLYSMH.EEEINKRQNARKIQIGSKGRSEKIRTYNFPQNRVTDHRINKTLHDLETFMQGDYLLD
Retrocopy MTKLRAKLYSMHVEEEINKRQNARKIQIGSKGRSEKIRTYNFPQNRVTDHRINKTLHDLETFMQGDYLLD

Parental  ELVQSLKEYADYESLVEIISQKV
          ELVQSLKEYA.YESLVEIISQKV
Retrocopy ELVQSLKEYANYESLVEIISQKV

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
bodymap2_adipose	2.19 RPM	11.93 RPM
bodymap2_adrenal	1.90 RPM	12.73 RPM
bodymap2_brain	0.89 RPM	15.63 RPM
bodymap2_breast	0.37 RPM	17.32 RPM
bodymap2_colon	2.88 RPM	14.02 RPM
bodymap2_heart	1.55 RPM	15.95 RPM
bodymap2_kidney	2.73 RPM	18.98 RPM
bodymap2_liver	0.74 RPM	8.37 RPM
bodymap2_lung	0.93 RPM	12.62 RPM
bodymap2_lymph_node	1.48 RPM	10.31 RPM
bodymap2_ovary	2.33 RPM	11.03 RPM
bodymap2_prostate	1.30 RPM	8.18 RPM
bodymap2_skeletal_muscle	1.25 RPM	9.75 RPM
bodymap2_testis	1.83 RPM	16.99 RPM
bodymap2_thyroid	0.81 RPM	22.69 RPM
bodymap2_white_blood_cells	0.85 RPM	10.85 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3018 was not detected

EST

2 EST(s) were mapped to retro_hsap_3018 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW363470	189660407	189660519	100	111	0	110
DB454169	189659525	189660013	99	483	5	478

TSS

No TSS is located nearby retro_hsap_3018 retrocopy 5' end.

Lab

retro_hsap_3018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3018 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	ENSCJAG00000012787	1 retrocopy	retro_cjac_1305,
Homo sapiens	ENSG00000112031	1 retrocopy	retro_hsap_3018 ,
Sarcophilus harrisii	ENSSHAG00000017997	1 retrocopy	retro_shar_129,
Ictidomys tridecemlineatus	ENSSTOG00000009980	1 retrocopy	retro_itri_335,
Tupaia belangeri	ENSTBEG00000003131	2 retrocopies	retro_tbel_2448, retro_tbel_4085,