RetrogeneDB ID: retro_pabe_1121

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:61504616..61505330(+)
• Located in intron of: ENSPPYG00000005876

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAD2L1
• Ensembl ID: ENSPPYG00000015029
• Aliases: None
• Description: MAD2 mitotic arrest deficient-like 1 (yeast) [Source:HGNC Symbol;Acc:6763]

Sequence

>retro_pabe_1121
GTCTTTACTTTTGAAACGCTTGGCGGGGAAGTGCTGTTGGAGCCGCTGTGGTTGCTGTCCGCGTAGTGAAAGCGCGTGCC
TTTGTTTGTGTTCCTGGCCATGGCGCTGCGGCTCTCCCGGGAGCAGGGAATCACCCTGCGCGGGAGTGCTGAAATCGTGG
CCGAGTTCTTCTCATTCGGCATCAACAGCATTTTATATCAGCGTGGCATTTATCCATCTGAAACCTTTACTCGAGTGCAG
AAATACGGACTCACCTTGCTTGTAACTACTGATCTTGATCTCATAAAATACCTAAATAATGTGGTAGAACAACTAAAAGA
TTGGTTATACAAGTGTTCAGTTCAGAAACTGGTTGTAGTTATCTCAAATATTGAAAGTGGTGAGGTCCTGGAAAGATGGC
AGTTTGATATTGAGTGTGACAAGACTGCAAAAGATGACAGTGCACCCAGAGAAAAGTCTCAGAAAGCTATCCAGGATGAA
ATCCGTTCAGTCATCAGACAGATCACAGCTACAGTGACATTTCTGCCACTGTTGGAAGTTTCTTGTTCACTTGTTCTGCT
GATTTACACAGACAAAGATTTGGTTGTACCTGAAAAATGGGAAGAGTCGGGACCACAGTTTATTACCAATTCTGAGGAAG
TCGGCCTTTGTTCATTTACTACTACAATCCACAAAGTAAATAGCATGGTGGCCTACAAAATTCCTGTCAATGAC

Alignment

ORF - retro_pabe_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.8 %
• Parental protein coverage: 79.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVTFETLGGEVLLEPLWLLSAEWKRVPLFVSLAMALQLSREQGITLRGSAEIVAEFFSFGINSILYQRGI
          V.TFETLGGEVLLEPLWLLSA..KRVPLFV.LAMAL.LSREQGITLRGSAEIVAEFFSFGINSILYQRGI
Retrocopy VFTFETLGGEVLLEPLWLLSA**KRVPLFVFLAMALRLSREQGITLRGSAEIVAEFFSFGINSILYQRGI

Parental  YPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECD
          YPSETFTRVQKYGLTLLVTTDL.LIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECD
Retrocopy YPSETFTRVQKYGLTLLVTTDLDLIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECD

Parental  KTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITN
          KTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCS..LLIYTDKDLVVPEKWEESGPQFITN
Retrocopy KTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSLVLLIYTDKDLVVPEKWEESGPQFITN

Parental  SEEVRLRSFTTTIHKVNSMVAYKIPVND
          SEEV.L.SFTTTIHKVNSMVAYKIPVND
Retrocopy SEEVGLCSFTTTIHKVNSMVAYKIPVND

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	1.22 RPM
SRP007412_cerebellum	0.24 RPM	1.82 RPM
SRP007412_heart	0.00 RPM	0.96 RPM
SRP007412_kidney	0.00 RPM	0.86 RPM
SRP007412_liver	0.00 RPM	0.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1121 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1121 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_925

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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,