RetrogeneDB ID: retro_ptro_2872

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:6827323..6827599(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039609
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPEL1
• Ensembl ID: ENSPTRG00000030224
• Aliases: None
• Description: None

Sequence

>retro_ptro_2872
ATGGCATACAGTGGCCAGGGCCAGAAAGTGCAGAAGGTTATGGTGCAGCCCATCAACCTCATCTTCAGATACTTACAAAA
TAGATCGCGGATTCAGGTGTGGCTCTATGAGCAAGTGAATATGCAGATAGAAGGCTGTATCATTGGTTTTGATGAGTATA
TGAACCTTGTATTAGATGATGCAGAAGAGATTCATTCTAAAACAAAGTCAAGAAAACAACTGGGTCGGATCATGCTAAAA
GGAGATAATATTACTCTGCTACAAAGTGTCTCCAAC

Alignment

ORF - retro_ptro_2872 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKS
          MAY.GQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNM.IEGCIIGFDEYMNLVLDDAEEIHSKTKS
Retrocopy MAYSGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMQIEGCIIGFDEYMNLVLDDAEEIHSKTKS

Parental  RKQLGRIMLKGDNITLLQSVSN
          RKQLGRIMLKGDNITLLQSVSN
Retrocopy RKQLGRIMLKGDNITLLQSVSN

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	0.52 RPM	11.39 RPM
SRP007412_cerebellum	0.18 RPM	6.20 RPM
SRP007412_heart	0.20 RPM	4.78 RPM
SRP007412_kidney	0.58 RPM	10.41 RPM
SRP007412_liver	0.43 RPM	5.30 RPM
SRP007412_testis	0.21 RPM	4.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2872 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2872 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2872 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4228
Gorilla gorilla	retro_ggor_91
Pongo abelii	retro_pabe_20

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 115 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009158	6 retrocopies	retro_chof_139, retro_chof_1870, retro_chof_1897, retro_chof_1981, retro_chof_2652, retro_chof_450,
Callithrix jacchus	ENSCJAG00000006735	1 retrocopy	retro_cjac_3163,
Dasypus novemcinctus	ENSDNOG00000004490	24 retrocopies	retro_dnov_1009, retro_dnov_1141, retro_dnov_122, retro_dnov_1223, retro_dnov_1312, retro_dnov_1314, retro_dnov_1362, retro_dnov_1438, retro_dnov_163, retro_dnov_191, retro_dnov_2398, retro_dnov_2671, retro_dnov_360, retro_dnov_414, retro_dnov_513, retro_dnov_579, retro_dnov_796, retro_dnov_828, retro_dnov_898, retro_dnov_900, retro_dnov_902, retro_dnov_93, retro_dnov_967, retro_dnov_983,
Echinops telfairi	ENSETEG00000014015	24 retrocopies	retro_etel_1136, retro_etel_1244, retro_etel_138, retro_etel_1443, retro_etel_1530, retro_etel_1636, retro_etel_1739, retro_etel_1781, retro_etel_1947, retro_etel_2143, retro_etel_234, retro_etel_258, retro_etel_310, retro_etel_377, retro_etel_466, retro_etel_546, retro_etel_56, retro_etel_579, retro_etel_581, retro_etel_582, retro_etel_76, retro_etel_776, retro_etel_799, retro_etel_80,
Felis catus	ENSFCAG00000000873	2 retrocopies	retro_fcat_1836, retro_fcat_554,
Homo sapiens	ENSG00000182004	10 retrocopies	retro_hsap_130, retro_hsap_1668, retro_hsap_2022, retro_hsap_2073, retro_hsap_2287, retro_hsap_3262, retro_hsap_4228, retro_hsap_4660, retro_hsap_516, retro_hsap_576,
Gorilla gorilla	ENSGGOG00000000755	7 retrocopies	retro_ggor_1462, retro_ggor_1626, retro_ggor_1700, retro_ggor_2221, retro_ggor_228, retro_ggor_2892, retro_ggor_91,
Microcebus murinus	ENSMICG00000015537	3 retrocopies	retro_mmur_1406, retro_mmur_453, retro_mmur_58,
Monodelphis domestica	ENSMODG00000028394	3 retrocopies	retro_mdom_1164, retro_mdom_1790, retro_mdom_1865,
Mustela putorius furo	ENSMPUG00000011642	7 retrocopies	retro_mputfur_1078, retro_mputfur_1527, retro_mputfur_1634, retro_mputfur_53, retro_mputfur_638, retro_mputfur_729, retro_mputfur_949,
Pongo abelii	ENSPPYG00000000326	8 retrocopies	retro_pabe_1375, retro_pabe_20, retro_pabe_2023, retro_pabe_228, retro_pabe_3015, retro_pabe_3620, retro_pabe_56, retro_pabe_610,
Pan troglodytes	ENSPTRG00000030224	11 retrocopies	retro_ptro_1131, retro_ptro_134, retro_ptro_1345, retro_ptro_1346, retro_ptro_1526, retro_ptro_1620, retro_ptro_2206, retro_ptro_2872 , retro_ptro_3096, retro_ptro_385, retro_ptro_426,
Sorex araneus	ENSSARG00000003311	9 retrocopies	retro_sara_171, retro_sara_173, retro_sara_183, retro_sara_214, retro_sara_219, retro_sara_37, retro_sara_664, retro_sara_697, retro_sara_750,