RetrogeneDB ID: retro_ggor_925

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 13:12397760..12398897(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000175354
• Ensembl ID: ENSGGOG00000010259
• Aliases: None
• Description: Tyrosine-protein phosphatase non-receptor type [Source:UniProtKB/TrEMBL;Acc:G3R421]

Sequence

>retro_ggor_925
ATGCCCACCATCATTGAGCGGGAGTTCGAGGAGTTGGATGCTCAGCATCGCTGGCAGCTGCCGTACTTGGAAATTCGAAA
TGAGTCCCATGACTATCTTCATAGAGTGGCCAAGTTTCCAGAAAACAGAAATCGAAATAGATACAGAGATGTAAGCCCAT
ATGATCACAGTCGTGTTAAACTGCAAAATACTGAGAATGATTATATTAATGCCAGCTTAGTTGACACAGAAGAGGCACGA
AGGAGTTACATCTGAACACAGGGTCCACTTCCTAACATGTGCTGCCATTTCTGGCTTACGGTTTGGCAGCAGAAGACCAA
AGCAGTTGTTGTGCTGAACCGCATTGCGGAGAAAGAATCGGTTAAATGTGCGCAGTACTGGCCAACAGATGACCAAAAGA
TGCTGTTTAAAGAAACGGGATTCAATGTGAAGCTCTTTCAGAAGATGTGAAGTCATATCACACAGTACATCTACTACGAT
TAGAAAATATCAATAGTGGTGAAACCAGAACAATATCTCACTTGTATTATACGACCTGGCCAGATTTTGGAGTCCCTGAA
TCAACAGCTTCATTTCTCAATTTCTTGTTGAAAGTGAGAGAATCTGGCTCCTTGAACCCTGACCACGGGCCTGCAGTGAT
CCATTGTAGTGAAGGCACTGGGTGCTCGGGCACCTGCTCTCTGGTAGACGCTTGTCTTGTTTTGATGGGAAAAGGAGATT
ATATTAACATTAAACAAGTGTTATTGAACAGGAGAAAATACTGAATGGGTCTTATTCAGACCCCAGATCAACTGACATTC
TCATACATGGCTATAATAGAAGGAGCAAAATGTATAAAGGTAGATTCTAGTATACAGAAACGGTGGAAAGAATTTTCTAA
GGAAAACTTAGCTCCCGCTTTTGATCATTCGCCAAACAAAATAATGACTGAAAAATACAATGGGAACAGAATTGGTCTAG
AAGAAGAAAAACTGACAGGTGACCGATGTACAGTAAATGCAAGATACAATGGAAGAGAACAGTGAGAATGCTCTACGGAA
ACATATTCTGGAGGAGAGAAAGGCCACCACAGCTCAGAAGGTGCAGCAGATGAAACAGAGGCTAAATGAGAACGAACAAA
AAAGAAAAAGGCCAAGA

Alignment

ORF - retro_ggor_925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.98 %
• Parental protein coverage: 91.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYIN
          MPT.IEREFEELD.Q.RWQ..YLEIRNESHDY.HRVAKFPENRNRNRYRDVSPYDHSRVKLQN.ENDYIN
Retrocopy MPTIIEREFEELDAQHRWQLPYLEIRNESHDYLHRVAKFPENRNRNRYRDVSPYDHSRVKLQNTENDYIN

Parental  ASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETG
          ASLVD.EEA.RSYI.TQGPLPN.CCHFWL.V................KESVKCAQYWPTDDQ.MLFKETG
Retrocopy ASLVDTEEARRSYI*TQGPLPNMCCHFWLTVXXXXXXXXXXXXXXXXKESVKCAQYWPTDDQKMLFKETG

Parental  FSVKL-LSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDH
          F.VKL.LSEDVKSY.TVHLL.LENINSGETRTISH..YTTWPDFGVPES.ASFLNFL.KVRESGSLNPDH
Retrocopy FNVKL<LSEDVKSYHTVHLLRLENINSGETRTISHLYYTTWPDFGVPESTASFLNFLLKVRESGSLNPDH

Parental  GPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCI
          GPAVIHCS.G.G.SGT.SLVD.CLVLM.KGD.INIKQVLLN.RKY.MGLIQTPDQL.FSYMAIIEGAKCI
Retrocopy GPAVIHCSEGTGCSGTCSLVDACLVLMGKGDYINIKQVLLNRRKY*MGLIQTPDQLTFSYMAIIEGAKCI

Parental  KGDSSIQKRWKELSKEDLSPAFDHSPNKIMTEKYNGNRIGLEEEKLTGDRCTG-LSSKMQDTMEENSESA
          K.DSSIQKRWKE.SKE.L.PAFDHSPNKIMTEKYNGNRIGLEEEKLTGDRCT......M....E......
Retrocopy KVDSSIQKRWKEFSKENLAPAFDHSPNKIMTEKYNGNRIGLEEEKLTGDRCTV>MQDTMEENSENALRKH

Parental  LRKRIREDRKATTAQKVQQMKQRLNENERKRKR
          ..............Q..Q......NE..RKR.R
Retrocopy ILEERKATTAQKVQQMKQRLNE--NEQKRKRPR

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	3.55 RPM
SRP007412_cerebellum	0.08 RPM	5.44 RPM
SRP007412_heart	0.06 RPM	0.66 RPM
SRP007412_kidney	0.04 RPM	6.87 RPM
SRP007412_liver	0.03 RPM	4.01 RPM
SRP007412_testis	0.00 RPM	9.22 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_925 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000867	1 retrocopy	retro_chof_2231,
Callithrix jacchus	ENSCJAG00000005102	1 retrocopy	retro_cjac_1577,
Dasypus novemcinctus	ENSDNOG00000016588	1 retrocopy	retro_dnov_1466,
Erinaceus europaeus	ENSEEUG00000005636	1 retrocopy	retro_eeur_370,
Echinops telfairi	ENSETEG00000005577	2 retrocopies	retro_etel_1743, retro_etel_1942,
Homo sapiens	ENSG00000175354	2 retrocopies	retro_hsap_1186, retro_hsap_480,
Gorilla gorilla	ENSGGOG00000010259	2 retrocopies	retro_ggor_453, retro_ggor_925 ,
Gorilla gorilla	ENSGGOG00000010689	1 retrocopy	retro_ggor_1962,
Loxodonta africana	ENSLAFG00000011818	1 retrocopy	retro_lafr_701,
Macropus eugenii	ENSMEUG00000005156	1 retrocopy	retro_meug_653,
Monodelphis domestica	ENSMODG00000021422	1 retrocopy	retro_mdom_1225,
Nomascus leucogenys	ENSNLEG00000009074	3 retrocopies	retro_nleu_2112, retro_nleu_351, retro_nleu_894,
Otolemur garnettii	ENSOGAG00000028605	1 retrocopy	retro_ogar_3429,
Pongo abelii	ENSPPYG00000008983	3 retrocopies	retro_pabe_1077, retro_pabe_1144, retro_pabe_989,
Pan troglodytes	ENSPTRG00000009884	2 retrocopies	retro_ptro_361, retro_ptro_813,