RetrogeneDB ID: retro_lafr_701

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_31:85854..86999(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000011818
• Aliases: None
• Description: Tyrosine-protein phosphatase non-receptor type [Source:UniProtKB/TrEMBL;Acc:G3T885]

Sequence

>retro_lafr_701
ATGTCCATCACCGTCCAGCGGGAGTTTGATGAGCTGGATGCTCGGAATTGTTGGCAGCAGCTGTACCTGGAAATTTGAAA
TGAGTCCCATGACTATCCTCATAGGGTGGTCAAGTTTCCAGAAAACAGAAATGGAAACAGATACAGAGATGTGAGCCCAT
ATGATCACAGTCGTGTTAAACTGCAAAATACTGAAAATGATTATATTAATGCCAGTTTAGTTGACATAGAAGAGGCACAA
AGGAGTTACATCTTAACACAGCGTTCACTTCCTAATACACGTTGTCATTTCTGGCTCATGGTTTGGCAGCAAAAGACCAA
AGCAATGGTCATGCTAAACTGAGTTGTAGAGAAGGAATCGGTTAAATGTGCACAGTACTGGCCAAAAAAGATGACCAAGA
GATGCTGTTTAAAGAAACAGTATTTATTGTGAAGTTCTTATCAGAAGATGTGAAATCATAGTATACGGTGCATCTACTAC
AACTAGAAAATACCAATAGTGGTGAAACCAGAACAATATCTCACTTTCATTGTACCACCTGGCCAGATTTTGGAGTCCCT
GAATCACTAGCTTCATTTCTCAATTTCTTATTTAAAGTGAGAGAATTTGGCTCCTTGAGCCCTGAGCATAGGACCGTTGT
AGTTCACTTCAGTGCCGGCATCGGGTGATCTGACACTTTTTCCCTAGTAGACAGCTGTCTGATTTTGATGGAAAAAGGAA
ATGATACTAACATTAAACAAGTATTACTGAACATGAGAAAATATCGAATAGGACTTATTCAGACACCAGATCAGCTCAGA
TTCTCATATATGGCTATAATAGAAGGAGTAAAGTTTATAAAGGGAGATTCAAACATACAGGAACTGTGGAAAGAGCTTTC
TAAGAAAGACTTGTCTCCTCCTTTTGATCATTCACCAACCAAAATAGTGACTGAAAGATACAATGGGAACAGAATGAGCT
TAGAAGAAGGAAAACTTACAGGTGACAGGTGTACAGGACTGTCCTCTGAAATGCAAAATACTGTAGAGGGAAAGAGTGAG
AGTGCTCTGCGGAAATGTATTCGAGAGGACAGAAAAGCTAACACTGTTCAGAAGGTGCGACAGATGAAGCAGAGGCTAAA
TGAGACTGAACGAAAAAGGCCAAGA

Alignment

ORF - retro_lafr_701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.77 %
• Parental protein coverage: 93.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVTVQREFDELDARNCWQQLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNTENDYIN
          MS.TVQREFDELDARNCWQQLYLEI.NESHDYPHRV.KFPENRN.NRYRDVSPYDHSRVKLQNTENDYIN
Retrocopy MSITVQREFDELDARNCWQQLYLEI*NESHDYPHRVVKFPENRNGNRYRDVSPYDHSRVKLQNTENDYIN

Parental  ASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTK-DDQEMLFKE
          ASLVDIEEAQRSYILTQ..LPNT.CHFWLMVWQQKTKA.VMLN..VEKESVKCAQYWP.K.DDQEMLFKE
Retrocopy ASLVDIEEAQRSYILTQRSLPNTRCHFWLMVWQQKTKAMVMLN*VVEKESVKCAQYWPKK<DDQEMLFKE

Parental  TGFIVKFLSEDVKSYYTVHLLQLENISSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPE
          T.FIVKFLSEDVKS.YTVHLLQLEN..SGETRTISHFH.TTWPDFGVPES.ASFLNFLFKVRE.GSL.PE
Retrocopy TVFIVKFLSEDVKS*YTVHLLQLENTNSGETRTISHFHCTTWPDFGVPESLASFLNFLFKVREFGSLSPE

Parental  HGPAIVHCSAGIGRSGTFSLVDTCLILMEKGNDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKF
          H....VH.SAGIG.S.TFSLVD.CLILMEKGND.NIKQVLLNMRKYR.GLIQTPDQLRFSYMAIIEG.KF
Retrocopy HRTVVVHFSAGIG*SDTFSLVDSCLILMEKGNDTNIKQVLLNMRKYRIGLIQTPDQLRFSYMAIIEGVKF

Parental  IKGDSNIQKRWKELSKEDLSPAFDHSPTKIVTERYNGNRMSLEEGKVTGDRCTGLSSKMQDTVEEKSESA
          IKGDSNIQ..WKELSK.DLSP.FDHSPTKIVTERYNGNRMSLEEGK.TGDRCTGLSS.MQ.TVE.KSESA
Retrocopy IKGDSNIQELWKELSKKDLSPPFDHSPTKIVTERYNGNRMSLEEGKLTGDRCTGLSSEMQNTVEGKSESA

Parental  LRKRIREDRKANTAQKVQQMKQRLNETERKRKR
          LRK.IREDRKANT.QKV.QMKQRLNETERKR.R
Retrocopy LRKCIREDRKANTVQKVRQMKQRLNETERKRPR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_701 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 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,
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,