RetrogeneDB ID: retro_ptro_925

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:59825749..59826361(+)
• Located in intron of: ENSPTRG00000006412

Retrocopy information

• Ensembl ID: ENSPTRG00000006414
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAD2L1
• Ensembl ID: ENSPTRG00000016401
• Aliases: None
• Description: None

Sequence

>retro_ptro_925
GCGCTGCAGCTCTCCCGGGAGCAGGGAATCACCCTGCGTGGGAGTGCCGAAATCGTGGCCGAGTTCTTCTCATTCGGCAT
CAACAGCATTTTATATCAGCGTGGCATTTATCCATCTGAAACCTTTACTCGAGTGCAGAAATACGGACTCACCTTGCTTG
TAACTACTGATCTTGAGCTCATAAAATACCTAAATAATGTGGTGGAACAACTAAAAGATTGGTTATACAAGTGTTCAGTT
CAGAAACTGGTTGTAGTTATCTCAAATATTGAAAGTGGTGAGGTCCTAGAAAGATGACAGTTTGATATTGAGTGTGACAA
GACTGCAAAAGATGACAGTGCACCCAGAGAAAAGTCTCAGAAAGCTATCCAGGATGAAATCCGTTCAGTCATCAGACAGA
TCACAGCTACAGTGACATTTCTGCCACTGTTGGAAGTTTCTTGTTCATTTGATCTGCTGATTTACACAGACAAAGATTTG
GTTGTACCTGAAAAATGGGAAGAGTCGGGATCACAGTTTATTACCAATTCTGAGGAAGTCTGCCTTTGTTCATTTACTAC
TACAATCCACAAAGTAAATAGCATGGTGGCCTACAAAATTCCTGTCAATGAC

Alignment

ORF - retro_ptro_925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.04 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQ
          ALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQ
Retrocopy ALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQ

Parental  LKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTF
          LKDWLYKCSVQKLVVVISNIESGEVLER.QFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTF
Retrocopy LKDWLYKCSVQKLVVVISNIESGEVLER*QFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTF

Parental  LPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND
          LPLLEVSCSFDLLIYTDKDLVVPEKWEESG.QFITNSEEV.L.SFTTTIHKVNSMVAYKIPVND
Retrocopy LPLLEVSCSFDLLIYTDKDLVVPEKWEESGSQFITNSEEVCLCSFTTTIHKVNSMVAYKIPVND

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	0.09 RPM	1.32 RPM
SRP007412_cerebellum	0.00 RPM	2.98 RPM
SRP007412_heart	0.06 RPM	1.19 RPM
SRP007412_kidney	0.08 RPM	1.15 RPM
SRP007412_liver	0.03 RPM	1.83 RPM
SRP007412_testis	0.00 RPM	15.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_925 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_925 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1121

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012813	2 retrocopies	retro_chof_1340, retro_chof_2524,
Dasypus novemcinctus	ENSDNOG00000013456	1 retrocopy	retro_dnov_1348,
Erinaceus europaeus	ENSEEUG00000009629	1 retrocopy	retro_eeur_446,
Echinops telfairi	ENSETEG00000015756	1 retrocopy	retro_etel_724,
Homo sapiens	ENSG00000164109	2 retrocopies	retro_hsap_1350, retro_hsap_1707,
Gorilla gorilla	ENSGGOG00000002516	1 retrocopy	retro_ggor_1281,
Loxodonta africana	ENSLAFG00000029619	1 retrocopy	retro_lafr_1138,
Myotis lucifugus	ENSMLUG00000011092	8 retrocopies	retro_mluc_1242, retro_mluc_165, retro_mluc_1802, retro_mluc_1904, retro_mluc_1986, retro_mluc_2434, retro_mluc_609, retro_mluc_696,
Macaca mulatta	ENSMMUG00000004875	2 retrocopies	retro_mmul_1292, retro_mmul_1701,
Mus musculus	ENSMUSG00000029910	2 retrocopies	retro_mmus_1684, retro_mmus_2573,
Nomascus leucogenys	ENSNLEG00000009092	1 retrocopy	retro_nleu_1832,
Otolemur garnettii	ENSOGAG00000004054	1 retrocopy	retro_ogar_199,
Pongo abelii	ENSPPYG00000015029	2 retrocopies	retro_pabe_1121, retro_pabe_1403,
Pan troglodytes	ENSPTRG00000016401	2 retrocopies	retro_ptro_1156, retro_ptro_925 ,
Ictidomys tridecemlineatus	ENSSTOG00000025410	2 retrocopies	retro_itri_1592, retro_itri_327,
Tupaia belangeri	ENSTBEG00000011065	3 retrocopies	retro_tbel_4460, retro_tbel_4666, retro_tbel_664,
Tursiops truncatus	ENSTTRG00000011017	1 retrocopy	retro_ttru_1754,